Help for package aroma.affymetrix

Version:

3.2.2

Depends:

R (≥ 3.2.0), R.utils (≥ 2.9.0), aroma.core (≥ 3.2.0)

Imports:

methods, R.methodsS3 (≥ 1.7.1), R.oo (≥ 1.23.0), R.cache (≥ 0.14.0), R.devices (≥ 2.16.1), R.filesets (≥ 2.13.0), aroma.apd (≥ 0.6.0), MASS, splines, matrixStats (≥ 0.55.0), listenv, future

Suggests:

DBI (≥ 1.0.0), gsmoothr (≥ 0.1.7), RColorBrewer (≥ 1.1-2), Biobase (≥ 2.28.0), BiocGenerics (≥ 0.14.0), affxparser (≥ 1.40.0), affy (≥ 1.46.0), affyPLM (≥ 1.44.0), aroma.light (≥ 2.4.0), gcrma (≥ 2.40.0), limma (≥ 3.24.1), oligo (≥ 1.32.0), oligoClasses (≥ 1.30.0), pdInfoBuilder (≥ 1.32.0), preprocessCore (≥ 1.28.0), AffymetrixDataTestFiles, dChipIO (≥ 0.1.1)

SuggestsNote:

BioC (>= 3.0), Recommended: preprocessCore, affyPLM, aroma.light, affxparser, DNAcopy

Title:

Analysis of Large Affymetrix Microarray Data Sets

Description:

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

License:

LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]

URL:

https://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.affymetrix

BugReports:

https://github.com/HenrikBengtsson/aroma.affymetrix/issues

LazyLoad:

TRUE

biocViews:

Infrastructure, ProprietaryPlatforms, ExonArray, Microarray, OneChannel, GUI, DataImport, DataRepresentation, Preprocessing, QualityControl, Visualization, ReportWriting, aCGH, CopyNumberVariants, DifferentialExpression, GeneExpression, SNP, Transcription

NeedsCompilation:

Packaged:

2024-02-18 19:43:01 UTC; henrik

Author:

Henrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb]

Maintainer:

Henrik Bengtsson <henrikb@braju.com>

Repository:

CRAN

Date/Publication:

2024-02-18 20:40:03 UTC

Package aroma.affymetrix

Description

Installation and updates

The preferred way to install this package is:

   source("https://callr.org/install#aroma.affymetrix")

To get started

To get started, see the online user guides and the vignettes https://www.aroma-project.org/.

How to cite this package

In order to keep improving and providing support for this project, please cite references [1], [2], or any applicable publication listed on https://aroma-project.org/publications/, whenever you publish work that have been used any of the Aroma Framework.

License

The releases of this package is licensed under LGPL version 2.1 or newer.

The development code of the packages is under a private license (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.

Author(s)

Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial, Elizabeth Purdom, Mark Robinson, Ken Simpson

References

[1] H. Bengtsson, K. Simpson, J. Bullard, and K. Hansen, aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008.
[2] H. Bengtsson, R. Irizarry, B. Carvalho, and T. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.
[3] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/

For a complete list, see https://aroma-project.org/publications/.

The AbstractProbeSequenceNormalization class

Description

Package: aroma.affymetrix
Class AbstractProbeSequenceNormalization

Directly known subclasses:
BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization

public abstract static class AbstractProbeSequenceNormalization
extends ProbeLevelTransform3

This abstract class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in probe sequences.

Usage

AbstractProbeSequenceNormalization(..., target=NULL)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform3.

target

A character string specifying type of "target" used. If "zero", all arrays are normalized to have no effects. If NULL, all arrays a normalized to have the same effect as the average array has.

Fields and Methods

Methods:

	`getTargetFile`	-
	`process`	-

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

Requirements

This class requires that an AromaCellSequenceFile is available for the chip type.

Author(s)

Henrik Bengtsson

The AdditiveCovariatesNormalization class

Description

Package: aroma.affymetrix
Class AdditiveCovariatesNormalization

Directly known subclasses:
GcContentNormalization2

public abstract static class AdditiveCovariatesNormalization
extends ChipEffectTransform

This class represents a normalization method that corrects for GC-content effects on copy-number chip-effect estimates.

Usage

AdditiveCovariatesNormalization(dataSet=NULL, ..., target=NULL, subsetToFit="-XY",
  shift=0, onMissing=c("median", "ignore"))

Arguments

dataSet

A SnpChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

target

(Optional) A character string or a function specifying what to normalize toward.

subsetToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

onMissing

Specifies how to normalize units for which the GC contents are unknown.

shift

An optional amount the data points should be shifted (translated).

Details

For SNPs, the normalization function is estimated based on the total chip effects, i.e. the sum of the allele signals. The normalizing is done by rescale the chip effects on the intensity scale such that the mean of the total chip effects are the same across samples for any given GC content. For allele-specific estimates, both alleles are always rescaled by the same amount. Thus, when normalizing allele-specific chip effects, the total chip effects is change, but not the relative allele signal, e.g. the allele B frequency.

Fields and Methods

Methods:

	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AffineCnPlm class

Description

Package: aroma.affymetrix
Class AffineCnPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffinePlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffineSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffineCnPlm

Directly known subclasses:

public abstract static class AffineCnPlm
extends CnPlm

Usage

AffineCnPlm(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to AffineSnpPlm.

combineAlleles

If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from AffineSnpPlm:
getAsteriskTags

Methods inherited from AffinePlm:
getAsteriskTags, getFitUnitGroupFunction, getProbeAffinityFile

Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AffinePlm class

Description

Package: aroma.affymetrix
Class AffinePlm

Directly known subclasses:
AffineCnPlm, AffineSnpPlm

public abstract static class AffinePlm
extends ProbeLevelModel

This class represents affine model in Bengtsson & Hossjer (2006).

Usage

AffinePlm(..., background=TRUE)

Arguments

...

Arguments passed to ProbeLevelModel.

background

If TRUE, background is estimate for each unit group, otherwise not. That is, if FALSE, a linear (proportional) model without offset is fitted, resulting in very similar results as obtained by the MbeiPlm.

Fields and Methods

Methods:

	`getProbeAffinityFile`	-

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

For a single unit group, the affine model is:

y_{ik} = a + \theta_i \phi_k + \varepsilon_{ik}

where a is an offset common to all probe signals, \theta_i are the chip effects for arrays i=1,...,I, and \phi_k are the probe affinities for probes k=1,...,K. The \varepsilon_{ik} are zero-mean noise with equal variance. The model is constrained such that \prod_k \phi_k = 1.

Note that with the additional constraint a=0 (see arguments above), the above model is very similar to MbeiPlm. The differences in parameter estimates is due to difference is assumptions about the error structure, which in turn affects how the model is estimated.

Author(s)

Henrik Bengtsson

References

Bengtsson & Hossjer (2006).

The AffineSnpPlm class

Description

Package: aroma.affymetrix
Class AffineSnpPlm

Directly known subclasses:
AffineCnPlm

public abstract static class AffineSnpPlm
extends SnpPlm

Usage

AffineSnpPlm(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to AffinePlm.

mergeStrands

If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from AffinePlm:
getAsteriskTags, getFitUnitGroupFunction, getProbeAffinityFile

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AffymetrixCdfFile class

Description

Package: aroma.affymetrix
Class AffymetrixCdfFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaChipTypeAnnotationFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitNamesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCdfFile

Directly known subclasses:

public abstract static class AffymetrixCdfFile
extends UnitNamesFile

An AffymetrixCdfFile object represents a generic Affymetrix CDF file.

Usage

AffymetrixCdfFile(...)

Arguments

...

Arguments passed to AromaChipTypeAnnotationFile.

Fields and Methods

Methods:

	`convert`	-
	`createExonByTranscriptCdf`	-
	`getACSFile`	-
	`getAromaCellSequenceFile`	-
	`getCellIndices`	-
	`getChipType`	-
	`getDimension`	-
	`getFileFormat`	-
	`getGenomeInformation`	-
	`getImage`	-
	`getPlatform`	-
	`getUnitNames`	-
	`getUnitTypes`	-
	`hasUnitTypes`	-
	`isMonocellCdf`	-
	`isPm`	-
	`isUniqueCdf`	-
	`nbrOfCells`	-
	`nbrOfColumns`	-
	`nbrOfQcUnits`	-
	`nbrOfRows`	-
	`nbrOfUnits`	-
	`readDataFrame`	-
	`readUnits`	-

Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits

Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith

Methods inherited from AromaChipTypeAnnotationFile:
as.character, byChipType, byName, findByChipType, fromFile, getChipType, getDefaultExtension, getHeader, getPlatform

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Author(s)

Henrik Bengtsson, Ken Simpson

Locates a CDF file from its chip type

Description

Locates a CDF file from its chip type.

Usage

## Static method (use this):
## AffymetrixCdfFile$findByChipType(chipType, tags=NULL, pattern=NULL, ...,
##   .useAffxparser=TRUE)

## Don't use the below:
## S3 method for class 'AffymetrixCdfFile'
findByChipType(static, chipType, tags=NULL, pattern=NULL, ..., .useAffxparser=TRUE)

Arguments

chipType

A character string.

tags

An optional character vector of tags.

pattern

An optional character string.

...

Not used.

.useAffxparser

If TRUE, findCdf is used if the CDF could not be located.

Value

Returns a pathname as a character string to the first CDF file found. If non CDF with requested chip type was found, NULL is returned.

Defines an AffymetrixCdfFile object from a CDF file

Description

Defines an AffymetrixCdfFile object from a CDF file.

Usage

## Static method (use this):
## AffymetrixCdfFile$fromFile(filename, path=NULL, ...)

## Don't use the below:
## S3 method for class 'AffymetrixCdfFile'
fromFile(static, filename, path=NULL, ...)

Arguments

filename

The filename of to the file.

path

The path to the file.

...

Not used.

Value

Returns an instance of AffymetrixCdfFile or its subclasses. If the file is not found or if it is of the wrong file format, an error is thrown.

The AffymetrixCelFile class

Description

Package: aroma.affymetrix
Class AffymetrixCelFile

Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile

public abstract static class AffymetrixCelFile
extends AffymetrixFile

An AffymetrixCelFile object represents a single Affymetrix CEL file.

Usage

AffymetrixCelFile(..., cdf=NULL)

Arguments

...

Arguments passed to AromaMicroarrayDataFile.

cdf

An optional AffymetrixCdfFile making it possible to override the default CDF file as specified by the CEL file header. The requirement is that its number of cells must match that of the CEL file. If NULL, the CDF structure is inferred from the the chip type as specified in the CEL file header.

Fields and Methods

Methods:

	`extractMatrix`	-
	`getAm`	-
	`getCdf`	-
	`getFileFormat`	-
	`getImage`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`image270`	-
	`nbrOfCells`	-
	`plotDensity`	-
	`plotImage`	-
	`plotMvsA`	-
	`plotMvsX`	-
	`setCdf`	-
	`smoothScatterMvsA`	-
	`writeImage`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

For developers

If you subclass this class, please make sure to query the AffymetrixCdfFile object (see *getCdf()) whenever querying CDF information. Do not use the CDF file inferred from the chip type in CEL header, unless you really want it to be hardwired that way, otherwise you will break to possibility to override the CDF structure.

Author(s)

Henrik Bengtsson

Creates an empty CEL file from a template CDF

Description

Creates an empty CEL file from a template CDF.

Usage

## Static method (use this):
## AffymetrixCelFile$allocateFromCdf(cdf, name, tags=NULL, path=".", suffix=".CEL", ...,
##   overwrite=FALSE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'AffymetrixCelFile'
allocateFromCdf(static, cdf, name, tags=NULL, path=".", suffix=".CEL", ...,
  overwrite=FALSE, verbose=FALSE)

Arguments

cdf

A AffymetrixCdfFile to be used as a template.

name, tags

The name and the tags of the file created.

path

The directory where the file is created.

suffix

Filename suffix.

...

Arguments passed to createCel.

overwrite

If FALSE and the file already exists, then an error is thrown.

verbose

See Verbose.

Value

Returns an AffymetrixCelFile.

Author(s)

Henrik Bengtsson

Clears all or a subset of the fields in a CEL file

Description

Clears all or a subset of the fields in a CEL file.

Usage

## Static method (use this):
## AffymetrixCelFile$clearData(fields=c("intensities", "stdvs", "pixels"), value=0, ...,
##   .forSure=FALSE, verbose=TRUE)

## Don't use the below:
## S3 method for class 'AffymetrixCelFile'
clearData(this, fields=c("intensities", "stdvs", "pixels"), value=0, ..., .forSure=FALSE,
  verbose=TRUE)

Arguments

fields

A character vector of fields to be cleared.

value

A numeric value to be written over the data.

...

Not used.

.forSure

If not TRUE, an exception is thrown asking if the method was called by mistake.

verbose

A logical or Verbose.

Value

Returns (invisibly) the names of the fields cleared.

Author(s)

Henrik Bengtsson

Defines an AffymetrixCelFile object from a CEL file

Description

Defines an AffymetrixCelFile object from a CEL file.

Usage

## Static method (use this):
## AffymetrixCelFile$fromFile(filename, path=NULL, ..., verbose=FALSE, .checkArgs=TRUE)

## Don't use the below:
## S3 method for class 'AffymetrixCelFile'
fromFile(static, filename, path=NULL, ..., verbose=FALSE, .checkArgs=TRUE)

Arguments

filename

The filename of to the file.

path

The path to the file.

...

Not used.

Value

Returns an AffymetrixCelFile object. If the file is not found or if it is of the wrong file format, an error is thrown.

Author(s)

Henrik Bengtsson

The AffymetrixCelSet class

Description

Package: aroma.affymetrix
Class AffymetrixCelSet

Directly known subclasses:
ChipEffectSet, CnChipEffectSet, ExonChipEffectSet, FirmaSet, ParameterCelSet, QualityAssessmentSet, ResidualSet, SnpChipEffectSet, WeightsSet

public static class AffymetrixCelSet
extends AffymetrixFileSet

An AffymetrixCelSet object represents a set of Affymetrix CEL files with identical chip types.

Usage

AffymetrixCelSet(files=NULL, ...)

Arguments

files

A list of AffymetrixCelFile:s.

...

Not used.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixCelSet`	-
	`byName`	-
	`doCRMAv1`	-
	`doCRMAv2`	-
	`doFIRMA`	-
	`doGCRMA`	-
	`doRMA`	-
	`extractAffyBatch`	-
	`extractFeatureSet`	-
	`extractMatrix`	-
	`getAverage`	-
	`getAverageAsinh`	-
	`getAverageFile`	-
	`getAverageLog`	-
	`getCdf`	-
	`getChipType`	-
	`getData`	-
	`getIntensities`	-
	`getPlatform`	-
	`getTimestamps`	-
	`getUnitGroupCellMap`	-
	`getUnitIntensities`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`justSNPRMA`	-
	`plotDensity`	-
	`readUnits`	-
	`setCdf`	-
	`writeSgr`	-

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName

Author(s)

Henrik Bengtsson

Examples

## Not run: 
  for (zzz in 0) {

# Find any dataset
path <- NULL
if (is.null(path))
  break

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define a dataset object based on all CEL files in a directory
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ds <- AffymetrixCelSet$fromFiles(path)
print(ds)

# Keep at most three arrays for this example
ds <- ds[1:min(3,nbrOfArrays(ds))]
print(ds)

} # for (zzz in 0)
rm(zzz)


## End(Not run)

Imports dChip-exported CEL files

Description

Imports dChip-exported CEL files into a directory structure recognized by this package. ASCII CEL files are converted to binary CEL files, and for chip types where the array data is rotated 90-degrees counter clockwise by dChip, the data is rotated back.

As of 2007-03-28, dChip rotates data for exon, tiling, and Mapping 500K arrays.

Usage

## Static method (use this):
## AffymetrixCelSet$importFromDChip(path, name=NULL, tags="dChip", rootPath="probeData",
##   rotateBack=NA, ..., skip=TRUE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'AffymetrixCelSet'
importFromDChip(static, path, name=NULL, tags="dChip", rootPath="probeData",
  rotateBack=NA, ..., skip=TRUE, verbose=FALSE)

Arguments

path

The path to all dChip-exported CEL files.

name

The name of the output data set. If NULL, the name is inferred from the source path.

tags

Tags added to the imported data set.

rootPath

The root path where to store the data set.

rotateBack

If TRUE, the dChip-rotated array data is rotated back. If NA, this is inferred from the chip type name.

...

Additional arguments passed to byPath().

skip

If TRUE, already converted files are not re-converted.

verbose

See Verbose.

Details

Note that dChip stores CEL intensities as 16-bit integers in its *.dcp files, although CEL files are capable or holding floats. This means that you might loose precision if first import data in to dChip and then export it data again.

Value

Returns an AffymetrixCelSet.

Author(s)

Henrik Bengtsson

The AffymetrixCelSetReporter class

Description

Package: aroma.affymetrix
Class AffymetrixCelSetReporter

Object
~~|
~~+--GenericReporter
~~~~~~~|
~~~~~~~+--AffymetrixFileSetReporter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AffymetrixCelSetReporter

Directly known subclasses:
SpatialReporter

public abstract static class AffymetrixCelSetReporter
extends AffymetrixFileSetReporter

Usage

AffymetrixCelSetReporter(..., .setClass="AffymetrixCelSet")

Arguments

...

Arguments passed to AffymetrixFileSetReporter.

.setClass

The name of the class of the input set.

Fields and Methods

Methods:

	`getDataSet`	-

Methods inherited from AffymetrixFileSetReporter:
getFileSet, getInputName, getInputTags

Methods inherited from GenericReporter:
as.character, getAlias, getAsteriskTags, getFullName, getInputName, getInputTags, getMainPath, getName, getPath, getReportSet, getRootPath, getTags, process, setAlias, setup

Author(s)

Henrik Bengtsson

The AffymetrixCelSetTuple class

Description

Package: aroma.affymetrix
Class AffymetrixCelSetTuple

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSetList
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSetTuple
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AffymetrixCelSetTuple

Directly known subclasses:
ChipEffectSetTuple, CnChipEffectSetTuple

public static class AffymetrixCelSetTuple
extends AromaMicroarrayDataSetTuple

Usage

AffymetrixCelSetTuple(..., .setClass="AffymetrixCelSet")

Arguments

...

Arguments passed to the constructor of AromaMicroarrayDataSetTuple.

.setClass

The name of the class of the input set.

Fields and Methods

Methods:

	`byPath`	-

Methods inherited from AromaMicroarrayDataSetTuple:
as, as.AromaMicroarrayDataSetTuple, byPath, getAsteriskTags, getChipTypes, getFullNames, getSets, getTags, indexOf, nbrOfChipTypes

Methods inherited from GenericDataFileSetList:
as, as.GenericDataFileSetList, as.character, as.data.frame, as.list, assertDuplicates, clone, extract, getAsteriskTags, getDefaultFullName, getFileList, getFileListClass, getFullNames, getNames, getSet, getSets, getTags, indexOf, length, nbrOfFiles, nbrOfSets, setTags

Author(s)

Henrik Bengtsson

The AffymetrixCnChpSet class

Description

Package: aroma.affymetrix
Class AffymetrixCnChpSet

Directly known subclasses:

public abstract static class AffymetrixCnChpSet
extends AffymetrixFileSet

A AffymetrixCnChpSet object represents a set of AffymetrixCnChpFile:s with identical chip types.

Usage

AffymetrixCnChpSet(files=NULL, ...)

Arguments

files

A list of AffymetrixCnChpFile:s.

...

Not used.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixCnChpSet`	-
	`exportTotalCnRatioSet`	-
	`extractLogRatios`	-
	`findByName`	-
	`getCdf`	-
	`setCdf`	-

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The abstract AffymetrixFile class

Description

Package: aroma.affymetrix
Class AffymetrixFile

Directly known subclasses:
AffymetrixCdfFile, AffymetrixCelFile, AffymetrixCnChpFile, AffymetrixPgfFile, AffymetrixTsvFile, AromaChipTypeAnnotationFile, ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, CnagCfhFile, DChipCdfBinFile, DChipDcpFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile

public abstract static class AffymetrixFile
extends AromaPlatformInterface

An AffymetrixFile object represents a single Affymetrix file, e.g. an Affymetrix CEL file or an Affymetrix CDF file. Note that this class is abstract and can not be instanciated, but instead you have to use one of the subclasses or the generic fromFile() method.

Usage

AffymetrixFile(...)

Arguments

...

Arguments passed to GenericDataFile.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The AffymetrixFileSet class

Description

Package: aroma.affymetrix
Class AffymetrixFileSet

Directly known subclasses:
AffymetrixCelSet, AffymetrixCnChpSet, ChipEffectSet, CnChipEffectSet, DChipDcpSet, ExonChipEffectSet, FirmaSet, ParameterCelSet, QualityAssessmentSet, ResidualSet, SnpChipEffectSet, WeightsSet

public abstract static class AffymetrixFileSet
extends AromaPlatformInterface

An AffymetrixFileSet object represents a set of AffymetrixFiles with identical chip types.

Usage

AffymetrixFileSet(files=NULL, ...)

Arguments

files

A list of AffymetrixFile:s.

...

Arguments passed to GenericDataFileSet.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixFileSet`	-
	`byPath`	-

Author(s)

Henrik Bengtsson

Defines an AffymetrixFileSet object by searching for Affymetrix files

Description

Defines an AffymetrixFileSet object by searching for Affymetrix files.

Usage

## Static method (use this):
## AffymetrixFileSet$byPath(..., fileClass="AffymetrixFile")

## Don't use the below:
## S3 method for class 'AffymetrixFileSet'
byPath(static, ..., fileClass="AffymetrixFile")

Arguments

...

Additional arguments passed to the constructor of the static (calling) class.

fileClass

The name of the GenericDataFile class.

Value

Returns an AffymetrixFileSet object.

Reserved filenames

Note that files with names starting with a period . are not searched for. The reason for this is that such files are reserved for internal use of this package. For instance, the package store average signals across CEL files in a file named as .average<something>.CEL in the same directory as the CEL files, and when such a directory is scanned we do not want such files to be interpreted as data.

The AffymetrixFileSetReporter class

Description

Package: aroma.affymetrix
Class AffymetrixFileSetReporter

Object
~~|
~~+--GenericReporter
~~~~~~~|
~~~~~~~+--AffymetrixFileSetReporter

Directly known subclasses:
AffymetrixCelSetReporter, SpatialReporter

public abstract static class AffymetrixFileSetReporter
extends GenericReporter

Usage

AffymetrixFileSetReporter(set=NULL, ..., .setClass="AffymetrixFileSet")

Arguments

set

An AffymetrixFileSet object.

...

Arguments passed to GenericReporter.

.setClass

The name of the class of the input set.

Fields and Methods

Methods:

	`getInputName`	-
	`getInputTags`	-

Author(s)

Henrik Bengtsson

The AffymetrixPgfFile class

Description

Package: aroma.affymetrix
Class AffymetrixPgfFile

Directly known subclasses:

public abstract static class AffymetrixPgfFile
extends UnitNamesFile

An AffymetrixPgfFile object represents a generic Affymetrix Probe Group File (PGF). A PGF file "provides information about what probes are contained within a probeset and information about the nature of the probes necessary for analysis. The current PGF file format (version 1) is only specified for expression style probesets." [1]

Usage

AffymetrixPgfFile(...)

Arguments

...

Arguments passed to AromaChipTypeAnnotationFile.

Fields and Methods

Methods:

	`getChipType`	-
	`getDimension`	-
	`getPlatform`	-
	`getUnitNames`	-
	`nbrOfCells`	-
	`nbrOfColumns`	-
	`nbrOfRows`	-
	`nbrOfUnits`	-

Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits

Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from AromaChipTypeAnnotationFile:
as.character, byChipType, byName, findByChipType, fromFile, getChipType, getDefaultExtension, getHeader, getPlatform

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

References

[1] ...

Locates a PGF file from its chip type

Description

Locates a PGF file from its chip type.

Usage

## Static method (use this):
## AffymetrixPgfFile$findByChipType(chipType, tags=NULL, pattern=NULL, ...)

## Don't use the below:
## S3 method for class 'AffymetrixPgfFile'
findByChipType(static, chipType, tags=NULL, pattern=NULL, ...)

Arguments

chipType

A character string.

tags

An optional character vector of tags.

pattern

An optional character string.

...

Not used.

Value

Returns a pathname as a character string to the first PGF file found. If non PGF with requested chip type was found, NULL is returned.

Defines an AffymetrixPgfFile object from a PGF file

Description

Defines an AffymetrixPgfFile object from a PGF file.

Usage

## Static method (use this):
## AffymetrixPgfFile$fromFile(filename, path=NULL, ...)

## Don't use the below:
## S3 method for class 'AffymetrixPgfFile'
fromFile(static, filename, path=NULL, ...)

Arguments

filename

The filename of to the file.

path

The path to the file.

...

Not used.

Value

Returns an instance of AffymetrixPgfFile or its subclasses. If the file is not found or if it is of the wrong file format, an error is thrown.

The AffymetrixProbeTabFile class

Description

Package: aroma.affymetrix
Class AffymetrixProbeTabFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--TabularTextFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixProbeTabFile

Directly known subclasses:

public abstract static class AffymetrixProbeTabFile
extends AromaPlatformInterface

An AffymetrixProbeTabFile represents an interface to query the data contained in an Affymetrix probe tab file, e.g. Mapping250K_Nsp_probe_tab.

Usage

AffymetrixProbeTabFile(...)

Arguments

...

Arguments passed to the constructor of AffymetrixFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getCdf`	-
	`getChipType`	-
	`getColumnNames`	-
	`getData`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from TabularTextFile:
as.character, getCommentChar, getDefaultColumnClassPatterns, getDefaultColumnClasses, getDefaultColumnNames, getHeader, getReadArguments, hasColumnHeader, nbrOfLines, nbrOfRows, readColumnNames, readColumns, readDataFrame, readLines, readRawHeader, setCommentChar

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames

About probe-tab files

Probe-tab files are provided by Affymetrix and contains information on the probes. Note that not necessarily all probes are represented in the files, e.g. typically only PM probes are given and MM are left to be inferred from the PMs.

The below is an extract of the Mapping250K_Nsp_probe_tab file obtained from the Affymetrix website. Note that columns are separated by TABs.

  SNP_A-1780270	1633	2398	3	TTGTTAAGCAAGTGAGTTATTTTAT	f	PM	C
  SNP_A-1780270	1633	2399	3	TTGTTAAGCAAGTGACTTATTTTAT	f	PM	G
  SNP_A-1780270	1951	1780	-4	GGATAAAATAAAATAACTCACTTGC	r	PM	C
  ...
  SNP_A-4241299	2553	1658	4	AAACACATTTTTGGGTCGTAAGGAA	f	PM	G

Author(s)

Henrik Bengtsson

The AlleleSummation class

Description

Package: aroma.affymetrix
Class AlleleSummation

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AlleleSummation

Directly known subclasses:

public abstract static class AlleleSummation
extends UnitModel

This class takes allele-specific chip effect estimates of a SnpChipEffectSet and returns a CnChipEffectSet holding the summed allele estimates.

Usage

AlleleSummation(dataSet=NULL, ignoreNAs=TRUE, ...)

Arguments

dataSet

A SnpChipEffectSet.

ignoreNAs

If TRUE, missing values are excluded when summing the signals from the two alleles.

...

Arguments passed to UnitModel.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getChipEffectSet`	-
	`process`	-

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AllelicCrosstalkCalibration class

Description

Package: aroma.affymetrix
Class AllelicCrosstalkCalibration

Directly known subclasses:

public static class AllelicCrosstalkCalibration
extends ProbeLevelTransform

This class represents a calibration function that transforms the probe-level signals such that the signals from the two alleles are orthogonal. The method fits and calibrates PM signals only. MM signals will not affect the model fitting and are unaffected.

Usage

AllelicCrosstalkCalibration(dataSet=NULL, ..., model=c("asis", "auto", "CRMA", "CRMAv2"),
  rescaleBy=c("auto", "groups", "all", "none"), targetAvg=c(2200, 2200),
  subsetToAvg="-XY", mergeShifts=TRUE, B=1, flavor=c("sfit", "expectile"),
  alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98, lambda=2,
  pairBy=c("CDF", "sequence"))

Arguments

dataSet

An AffymetrixCelSet.

...

Arguments passed to the constructor of ProbeLevelTransform.

model

A character string for quickly specifying default parameter settings.

rescaleBy

A character string specifying what sets of cells should be rescaled towards a target average, if any. Default is to rescale all cells together. If "none", no rescaling is done.

targetAvg

The signal(s) that either the average of the sum (if one target value) or the average of each of the alleles (if two target values) should have after calibration. Only used if rescaleBy != "none".

subsetToAvg

The indices of the cells (taken as the intersect of existing indices) used to calculate average in order to rescale to the target average. If NULL, all probes are considered.

mergeShifts

If TRUE, the shift of the probe sequence relative to the SNP position is ignored, otherwise not.

B

An integer specifying by how many nucleotides the allelic groups should be stratified by. If zero, all SNPs are put in one group.

flavor

A character string specifying what algorithm is used to fit the crosstalk calibration.

alpha, q, Q, lambda

Model fitting parameters.

pairBy

A character string specifying how allele probe pairs are identified.

What probe signals are updated?

Calibration for crosstalk between allele signals applies by definition only SNP units. Furthermore, it is only SNP units with two or four unit groups that are calibrated. For instance, in at least on custom SNP CDFs we know of, there is a small number of SNP units that have six groups. Currently these units are not calibrated (at all). It is only PM probes that will be calibrated. Note that, non-calibrated signals will be saved in the output files.

What probe signals are used to fit model?

All PM probe pairs are used to fit the crosstalk model. In the second step where signals are rescaled to a target average, it is possible to specify the set of cells that should be included when estimating the target average.

Important about rescaling towards target average

Rescaling each allele-pair group (e.g. AC, AG, AT, CG, CT, GC) towards a target average (rescaleBy="groups") must not be used for multi-enzyme chip types, e.g. GenomeWideSNP_6. If still done, due to confounded effects of non-perfect enzyme mixtures etc, there will be a significant bias between raw CNs for SNPs and CN probes. Instead, for such chip types all probe signals should be rescale together towards the target average (rescaleBy="all").

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AromaChipTypeAnnotationFile class

Description

Package: aroma.affymetrix
Class AromaChipTypeAnnotationFile

Directly known subclasses:
AffymetrixCdfFile, AffymetrixPgfFile

public abstract static class AromaChipTypeAnnotationFile
extends AffymetrixFile

An AromaChipTypeAnnotationFile object represents an annotation file for a specific chip type.

Usage

AromaChipTypeAnnotationFile(...)

Arguments

...

Arguments passed to AffymetrixFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getHeader`	-
	`getPlatform`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

Defines an AromaChipTypeAnnotationFile object by chip type

Description

Defines an AromaChipTypeAnnotationFile object by chip type.

Usage

## Static method (use this):
## AromaChipTypeAnnotationFile$byChipType(chipType, tags=NULL, ..., verbose=FALSE)

## Don't use the below:
## S3 method for class 'AromaChipTypeAnnotationFile'
byChipType(static, chipType, tags=NULL, ..., verbose=FALSE)

Arguments

chipType

A character string.

tags

An optional character vector of tags.

...

Not used.

verbose

See Verbose.

Value

Returns an AromaChipTypeAnnotationFile object.

Sets up an AromaChipTypeAnnotationFile

Description

Sets up an AromaChipTypeAnnotationFile.

Usage

## Static method (use this):
## AromaChipTypeAnnotationFile$fromFile(filename, path=NULL, ...)

## Don't use the below:
## S3 method for class 'AromaChipTypeAnnotationFile'
fromFile(static, filename, path=NULL, ...)

Arguments

filename

The filename of to the file.

path

The path to the file.

...

Not used.

Value

Returns an instance of AromaChipTypeAnnotationFile or its subclasses. If the file is not found or if it is of the wrong file format, an error is thrown.

Creates an AromaUnitTabularBinaryFile mapping to a given CDF

Description

Creates an AromaUnitTabularBinaryFile mapping to a given CDF.

Usage

## Static method (use this):
## AromaUnitTabularBinaryFile$allocateFromCdf(cdf, ...)

## Don't use the below:
## S3 method for class 'AromaUnitTabularBinaryFile'
allocateFromCdf(static, cdf, ...)

Arguments

cdf

The AffymetrixCdfFile used as a template and from which the (full) chip type is taken.

...

Additional arguments passed to allocate() of AromaTabularBinaryFile.

Value

Returns a AromaUnitTabularBinaryFile object.

Author(s)

Henrik Bengtsson

The ArrayExplorer class

Description

Package: aroma.affymetrix
Class ArrayExplorer

Object
~~|
~~+--Explorer
~~~~~~~|
~~~~~~~+--ArrayExplorer

Directly known subclasses:

public abstract static class ArrayExplorer
extends Explorer

Usage

ArrayExplorer(csTuple=NULL, ...)

Arguments

csTuple

An AffymetrixCelSet object.

...

Not used.

Fields and Methods

Methods:

	`addColorMap`	-
	`getColorMaps`	-
	`getDataSet`	-
	`getSetTuple`	-
	`nbrOfChipTypes`	-
	`process`	-
	`setArrays`	-
	`setColorMaps`	-

Methods inherited from Explorer:
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile

Author(s)

Henrik Bengtsson

The AvgCnPlm class

Description

Package: aroma.affymetrix
Class AvgCnPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AvgPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AvgSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AvgCnPlm

Directly known subclasses:

public abstract static class AvgCnPlm
extends CnPlm

Usage

AvgCnPlm(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to AvgSnpPlm.

combineAlleles

If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from AvgSnpPlm:
getAsteriskTags

Methods inherited from AvgPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, validate

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AvgPlm class

Description

Package: aroma.affymetrix
Class AvgPlm

Directly known subclasses:
AvgCnPlm, AvgSnpPlm

public abstract static class AvgPlm
extends ProbeLevelModel

This class represents a PLM where the probe intensities are averaged assuming identical probe affinities. For instance, one may assume that replicated probes with identical sequences have the same probe affinities, cf. the GenomeWideSNP_6 chip type.

Usage

AvgPlm(..., flavor=c("median", "mean"))

Arguments

...

Arguments passed to ProbeLevelModel.

flavor

A character string specifying what model fitting algorithm to be used. This makes it possible to get identical estimates as other packages.

Fields and Methods

Methods:
No methods defined.

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

For a single unit group, the averaging PLM of K probes is:

y_{ik} = \theta_i + \varepsilon_{ik}

where \theta_i are the chip effects for arrays i=1,...,I. The \varepsilon_{ik} are zero-mean noise with equal variance.

Different flavors of model fitting

The above model can be fitted in two ways, either robustly or non-robustly. Use argument flavor="mean" to fit the model non-robustly, i.e.

\hat{\theta}_{i} = 1/K \sum_k y_{ik}

Use argument flavor="median" to fit the model robustly, i.e.

\hat{\theta}_{i} = median_k y_{ik}

Missing values are always excluded.

Author(s)

Henrik Bengtsson

The AvgSnpPlm class

Description

Package: aroma.affymetrix
Class AvgSnpPlm

Directly known subclasses:
AvgCnPlm

public abstract static class AvgSnpPlm
extends SnpPlm

Usage

AvgSnpPlm(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to AvgPlm.

mergeStrands

If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from AvgPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, validate

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The BackgroundCorrection class

Description

Package: aroma.affymetrix
Class BackgroundCorrection

Directly known subclasses:
GcRmaBackgroundCorrection, LimmaBackgroundCorrection, NormExpBackgroundCorrection, OpticalBackgroundCorrection, RmaBackgroundCorrection

public abstract static class BackgroundCorrection
extends ProbeLevelTransform

This class represents a background adjustment function.

Usage

BackgroundCorrection(..., subsetToUpdate=NULL, typesToUpdate=NULL)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

subsetToUpdate

The probes to be updated. If NULL, all probes are updated.

typesToUpdate

Types of probes to be updated.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson, Henrik Bengtsson

The BaseCountNormalization class

Description

Package: aroma.affymetrix
Class BaseCountNormalization

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--BaseCountNormalization

Directly known subclasses:

public static class BaseCountNormalization
extends AbstractProbeSequenceNormalization

This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in the number of A, C, G, and T:s in the probe sequences.

Usage

BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)

Arguments

...

Arguments passed to the constructor of AbstractProbeSequenceNormalization.

model

A character string specifying the model used to fit the base-count effects.

bootstrap

If TRUE, the model fitting is done by bootstrap in order to save memory.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires that an aroma probe sequence file is available for the chip type.

Author(s)

Henrik Bengtsson

The BasePositionNormalization class

Description

Package: aroma.affymetrix
Class BasePositionNormalization

Directly known subclasses:

public abstract static class BasePositionNormalization
extends LinearModelProbeSequenceNormalization

This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in positioning of A, C, G, and T:s in the probe sequences.

Usage

BasePositionNormalization(..., model=c("smooth.spline"), df=5)

Arguments

...

Arguments passed to the constructor of LinearModelProbeSequenceNormalization.

model

A character string specifying the model used to fit the base-count effects.

df

The degrees of freedom of the model.

Fields and Methods

Methods:
No methods defined.

Methods inherited from LinearModelProbeSequenceNormalization:
fitOne, getDesignMatrix, getNormalEquations, getSignalTransform, predictOne

Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson, Mark Robinson

The ChipEffectFile class

Description

Package: aroma.affymetrix
Class ChipEffectFile

Directly known subclasses:
CnChipEffectFile, ExonChipEffectFile, SnpChipEffectFile

public abstract static class ChipEffectFile
extends ParameterCelFile

This class represents estimates of chip effects in the probe-level models.

Usage

ChipEffectFile(..., probeModel=c("pm"))

Arguments

...

Arguments passed to ParameterCelFile.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods:

	`extractMatrix`	-
	`extractTheta`	-
	`findUnitsTodo`	-
	`getAM`	-
	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

Retrieve an existing CEL file, or create from CDF template if missing

Description

Retrieve an existing CEL file, or create from CDF template if missing.

Usage

## Static method (use this):
## ChipEffectFile$fromDataFile(df=NULL, filename=sprintf("%s,chipEffects.CEL",
##   getFullName(df)), path, name=getName(df), cdf=NULL, ..., verbose=FALSE)

## Don't use the below:
## S3 method for class 'ChipEffectFile'
fromDataFile(static, df=NULL, filename=sprintf("%s,chipEffects.CEL", getFullName(df)),
  path, name=getName(df), cdf=NULL, ..., verbose=FALSE)

Arguments

static

df

filename

The filename of the CEL file.

path

The path to the directory where to find/create the CEL file.

name

The name of the array to be stored in the CEL header.

cdf

The template AffymetrixCdfFile used for creating a CEL file from scratch.

...

Passed to createCel.

verbose

See Verbose.

Value

Returns a ChipEffectFile.

Author(s)

Henrik Bengtsson

The ChipEffectGroupMerge class

Description

Package: aroma.affymetrix
Class ChipEffectGroupMerge

Directly known subclasses:
SnpChipEffectGroupMerge

public static class ChipEffectGroupMerge
extends ChipEffectTransform

This class represents a method that merges chip effects across groups unit by unit.

Usage

ChipEffectGroupMerge(dataSet=NULL, fcn=NULL, ...)

Arguments

dataSet

A ChipEffectSet.

fcn

A function used to "merge" groups.

...

Additional arguments passed to the constructor of ChipEffectTransform.

Fields and Methods

Methods:

	`getCdf`	-
	`getMergeFunction`	-
	`process`	-
	`setMergeFunction`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ChipEffectSet class

Description

Package: aroma.affymetrix
Class ChipEffectSet

Directly known subclasses:
CnChipEffectSet, ExonChipEffectSet, SnpChipEffectSet

public static class ChipEffectSet
extends ParameterCelSet

This class represents estimates of chip effects in the probe-level models.

Usage

ChipEffectSet(..., probeModel=c("pm"))

Arguments

...

Arguments passed to AffymetrixCelSet.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods:

	`boxplotStats`	-
	`extractExpressionSet`	-
	`extractMatrix`	-
	`extractTheta`	-
	`findUnitsTodo`	-
	`getAM`	-
	`getAverageFile`	-
	`getCellIndices`	-
	`plotBoxplot`	-
	`readUnits`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The ChipEffectTransform class

Description

Package: aroma.affymetrix
Class ChipEffectTransform

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ChipEffectTransform

Directly known subclasses:
AdditiveCovariatesNormalization, ChipEffectGroupMerge, FragmentEquivalentClassNormalization, FragmentLengthNormalization, GcContentNormalization, GcContentNormalization2, SnpChipEffectGroupMerge

public abstract static class ChipEffectTransform
extends Transform

This abstract class represents a transform that transforms chip-effect estimates obtained from probe-level modeling.

Usage

ChipEffectTransform(dataSet=NULL, ...)

Arguments

dataSet

The input data set as an ChipEffectSet.

...

Arguments passed to the constructor of Transform.

Details

Subclasses must implement the process() method.

Fields and Methods

Methods:
No methods defined.

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The CnChipEffectFile class

Description

Package: aroma.affymetrix
Class CnChipEffectFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnChipEffectFile

Directly known subclasses:

public abstract static class CnChipEffectFile
extends CopyNumberDataFile

This class represents estimates of chip effects in a copy-number probe-level models.

Usage

CnChipEffectFile(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to SnpChipEffectFile.

combineAlleles

A logical indicating if the signals from allele A and allele B are combined or not.

Fields and Methods

Methods:

	`exportTotalAndFracB`	-
	`extractTheta`	-
	`extractTotalAndFreqB`	-
	`hasAlleleBFractions`	-
	`hasStrandiness`	-
	`mergeStrands`	-
	`readUnits`	-

Methods inherited from CopyNumberDataFile:
as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness

Methods inherited from SnpChipEffectFile:
exportTotalAndFracB, extractCNT, extractTheta, extractTotalAndFracB, getCellIndices, getExpandedCellMap, getParameters, mergeStrands, readUnits, writeCNT

Methods inherited from ChipEffectFile:
as.character, extractChromosomalDataFrame, extractMatrix, extractTheta, findUnitsTodo, getAM, getAsFullCelFile, getCellIndices, getCellMapForMainCdf, getExpandedCellMap, getParameters, getUnitGroupCellArrayMap, getUnitGroupCellMatrixMap, getXAM, mergeGroups, readUnits, writeAsFullCelFile

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The CnChipEffectSet class

Description

Package: aroma.affymetrix
Class CnChipEffectSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnChipEffectSet

Directly known subclasses:

public static class CnChipEffectSet
extends CopyNumberDataSet

This class represents estimates of chip effects in the probe-level models.

Usage

CnChipEffectSet(..., combineAlleles="byFirstFile")

Arguments

...

Arguments passed to SnpChipEffectSet.

combineAlleles

A logical indicating if the signals from allele A and allele B are combined or not.

Fields and Methods

Methods:

	`as.CopyNumberDataSetTuple`	-
	`exportTotalAndFracB`	-
	`extractTheta`	-
	`extractTotalAndFreqB`	-
	`getAverageFile`	-
	`getCombineAlleles`	-
	`hasAlleleBFractions`	-
	`hasStrandiness`	-
	`setCombineAlleles`	-
	`writeWig`	-

Methods inherited from CopyNumberDataSet:
as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness

Methods inherited from SnpChipEffectSet:
byPath, exportTotalAndFracB, extractAlleleSet, extractCNT, extractSnpCnvQSet, extractSnpQSet, extractTheta, extractTotalAndFreqB, getAverageFile, getBaseline, getMergeStrands, setMergeStrands, writeCNT

Methods inherited from ChipEffectSet:
as.character, boxplotStats, byPath, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractAffyBatch, extractChromosomalDataFrame, extractExpressionSet, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getXAM, plotBoxplot, readUnits, updateUnits

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

Imports copy-number estimates from an APT summary file

Description

Imports copy-number estimates from an APT summary file. Currently only total copy-number estimates can be imported.

Usage

## Static method (use this):
## CnChipEffectSet$importFromApt(filename, path=NULL, combineAlleles=TRUE, cdf, ...,
##   skip=TRUE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'CnChipEffectSet'
importFromApt(static, filename, path=NULL, combineAlleles=TRUE, cdf, ..., skip=TRUE,
  verbose=FALSE)

Arguments

filename

The filename of the APT summary file.

path

An optional path to the file.

combineAlleles

If TRUE, ...

cdf

An AffymetrixCdfFile object.

...

Not used.

skip

If TRUE, already imported arrays will be skipped.

verbose

See Verbose.

Details

This import method is robust and memory efficient. One array at the time is imported by first writing to a temporary file which is then renamed to the final name, if import was successful. (If the import failed, a temporary file will rename that has to be deleted manually).

Since only one array at the time is imported, the memory overhead will be bounded allowing to import very large tab-delimited data files containing a large number of arrays. Unfortunately, this approach slows down the reading substantially, because in each import all but one column is parsed but ignored.

Value

Returns an CnChipEffectSet.

Author(s)

Henrik Bengtsson

Imports copy-number estimates from a dChip result file

Description

Imports copy-number estimates from a dChip result file. Currently only total copy-number estimates can be imported, that is if dChip fitted the PLM with allele A and allele B combined.

Usage

## Static method (use this):
## CnChipEffectSet$importFromDChip(filename, path=NULL, combineAlleles=TRUE, cdf, ...,
##   skip=TRUE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'CnChipEffectSet'
importFromDChip(static, filename, path=NULL, combineAlleles=TRUE, cdf, ..., skip=TRUE,
  verbose=FALSE)

Arguments

filename

The filename of the dChip result file.

path

An optional path to the file.

combineAlleles

If TRUE, ...

cdf

An AffymetrixCdfFile object.

...

Not used.

skip

If TRUE, already imported arrays will be skipped.

verbose

See Verbose.

Details

Value

Returns an CnChipEffectSet.

Author(s)

Henrik Bengtsson

The CnPlm class

Description

Package: aroma.affymetrix
Class CnPlm

Interface
~~|
~~+--SnpPlm
~~~~~~~|
~~~~~~~+--CnPlm

Directly known subclasses:
AffineCnPlm, AvgCnPlm, HetLogAddCnPlm, MbeiCnPlm, RmaCnPlm

public class CnPlm
extends SnpPlm

This support class represents a SnpPlm specially designed for copy-number analysis.

Usage

CnPlm(...)

Arguments

...

Arguments passed to SnpPlm.

Details

Models implementing this copy-number PLM, provides either allele-specific or total copy-number estimates. For allele-specific CNs the underlying SnpPlm model is fitted as is, i.e. for each allele separately with or without the strands first being merged.

For total CNs the probe signals for the two alleles are combined (=summed; not averaged) on the intensity scale before fitting underlying SnpPlm model, again with or without the strands first being merged.

Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getCombineAlleles`	-
	`getProbeAffinityFile`	-
	`setCombineAlleles`	-

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from Interface:
extend, print, uses

Requirements

Classes inheriting from this Interface must provide the following fields, in addition to the ones according to SnpPlm:

combineAlleles: A logical indicating if total or allele-specific copy numbers should be estimated according to the above averaging.

Author(s)

Henrik Bengtsson

The CnProbeAffinityFile class

Description

Package: aroma.affymetrix
Class CnProbeAffinityFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnProbeAffinityFile

Directly known subclasses:

public abstract static class CnProbeAffinityFile
extends SnpProbeAffinityFile

This class represents estimates of probe affinities in SNP probe-level models.

Usage

CnProbeAffinityFile(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to SnpProbeAffinityFile.

combineAlleles

If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpProbeAffinityFile:
getCellIndices, setMergeStrands

Methods inherited from ProbeAffinityFile:
as.character, getCellIndices, getParameters, readUnits

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The CnagCfhFile class

Description

Package: aroma.affymetrix
Class CnagCfhFile

Directly known subclasses:

public abstract static class CnagCfhFile
extends AffymetrixFile

A CnagCfhFile object represents a single CNAG CFH file.

Usage

CnagCfhFile(..., cdf=NULL)

Arguments

...

Arguments passed to AromaMicroarrayDataFile.

cdf

An optional AffymetrixCdfFile

Fields and Methods

Methods:

	`getCdf`	-
	`nbrOfCells`	-
	`nbrOfSnps`	-
	`setCdf`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

Defines an CnagCfhFile object from a CFH file

Description

Defines an CnagCfhFile object from a CFH file.

Usage

## Static method (use this):
## CnagCfhFile$fromFile(filename, path=NULL, ..., verbose=FALSE, .checkArgs=TRUE)

## Don't use the below:
## S3 method for class 'CnagCfhFile'
fromFile(static, filename, path=NULL, ..., verbose=FALSE, .checkArgs=TRUE)

Arguments

filename

The filename of to the file.

path

The path to the file.

...

Not used.

Value

Returns an CnagCfhFile object. If the file is not found or if it is of the wrong file format, an error is thrown.

The CnagCfhSet class

Description

Package: aroma.affymetrix
Class CnagCfhSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CnagCfhSet

Directly known subclasses:

public static class CnagCfhSet
extends GenericDataFileSet

An CnagCfhSet object represents a set of CNAG CFH files with identical chip types.

Usage

CnagCfhSet(files=NULL, ...)

Arguments

files

A list of CnagCfhFile:s.

...

Not used.

Fields and Methods

Methods:

	`as`	-
	`as.CnagCfhSet`	-
	`byName`	-
	`getAverage`	-
	`getAverageAsinh`	-
	`getAverageFile`	-
	`getAverageLog`	-
	`getCdf`	-
	`getData`	-
	`getTimestamps`	-
	`readUnits`	-
	`setCdf`	-

Author(s)

Henrik Bengtsson

The CrlmmParametersFile class

Description

Package: aroma.affymetrix
Class CrlmmParametersFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CrlmmParametersFile

Directly known subclasses:

public static class CrlmmParametersFile
extends AromaUnitSignalBinaryFile

An CrlmmParametersFile is a AromaUnitSignalBinaryFile.

Usage

CrlmmParametersFile(...)

Arguments

...

Arguments passed to AromaUnitSignalBinaryFile.

Fields and Methods

Methods:

	`allocate`	-
	`findUnitsTodo`	-
	`readParameter`	-
	`updateParameter`	-

Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame

Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Author(s)

Henrik Bengtsson

The CrlmmParametersSet class

Description

Package: aroma.affymetrix
Class CrlmmParametersSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CrlmmParametersSet

Directly known subclasses:

public static class CrlmmParametersSet
extends AromaUnitSignalBinarySet

An CrlmmParametersSet object represents a set of CrlmmParametersFiles with identical chip types.

Usage

CrlmmParametersSet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

Methods:

	`byName`	-
	`byPath`	-
	`findUnitsTodo`	-

Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame

Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags

Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles

Author(s)

Henrik Bengtsson

The DChipCdfBinFile class

Description

Package: aroma.affymetrix
Class DChipCdfBinFile

Directly known subclasses:

public abstract static class DChipCdfBinFile
extends UnitNamesFile

A DChipCdfBinFile object represents a DChip CDF.bin file.

Usage

DChipCdfBinFile(...)

Arguments

...

Arguments passed to AffymetrixFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getFileFormat`	-
	`getHeader`	-
	`getPlatform`	-
	`getUnitNames`	-
	`getUnitSizes`	-
	`nbrOfCells`	-
	`nbrOfUnits`	-
	`readDataFrame`	-

Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits

Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The DChipDcpFile class

Description

Package: aroma.affymetrix
Class DChipDcpFile

Directly known subclasses:

public abstract static class DChipDcpFile
extends AffymetrixFile

A DChipDcpFile object represents a DChip DCP file.

Usage

DChipDcpFile(...)

Arguments

...

Arguments passed to AffymetrixFile.

Fields and Methods

Methods:

	`dim`	-
	`extractTheta`	-
	`getCalls`	-
	`getExcludes`	-
	`getFileFormat`	-
	`getHeader`	-
	`getNormalizedIntensities`	-
	`getRawIntensities`	-
	`getThetaStds`	-
	`getThetas`	-
	`getThetasAB`	-
	`hasMbeiData`	-
	`hasNormalizedData`	-
	`nbrOfCells`	-
	`nbrOfUnits`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The DChipDcpSet class

Description

Package: aroma.affymetrix
Class DChipDcpSet

Directly known subclasses:

public abstract static class DChipDcpSet
extends AffymetrixFileSet

A DChipDcpSet object represents a set of DChip DCP files for identical chip types.

Usage

DChipDcpSet(files=NULL, ...)

Arguments

files

A list of DChipDcpFile:s.

...

Not used.

Fields and Methods

Methods:

	`as`	-
	`as.DChipDcpSet`	-
	`byName`	-
	`exportTotalAndFracB`	-
	`extractTheta`	-
	`getCdfBin`	-
	`getChipType`	-

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The DChipGenomeInformation class

Description

Package: aroma.affymetrix
Class DChipGenomeInformation

Directly known subclasses:

public abstract static class DChipGenomeInformation
extends GenomeInformation

This class represents dChip genome information files, which typically contains information about chromosomal locations of the units.

Usage

DChipGenomeInformation(...)

Arguments

...

Arguments passed to GenomeInformation.

Details

The dChip genome information files for various chip types can be downloaded from https://sites.google.com/site/dchipsoft/. Put each file in a directory named identically as the corresponding chip type under the annotations/ directory, e.g. annotations/Mapping50K_Hind240/50k hind genome info AfAm june 05 hg17.xls. Note that dChip changes the filename and file format slightly between chip types, but currently the *byChipType() basically searches for files with names consisting of "genome info" or "genome_info". At least for the most common chip types, there is no need to rename the files in order for this class to recognize them.

Fields and Methods

Methods:

	`byChipType`	-
	`readDataFrame`	-

Methods inherited from GenomeInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getChromosomeStats, getChromosomes, getData, getPositions, getUnitIndices, getUnitsOnChromosome, getUnitsOnChromosomes, isCompatibleWithCdf, nbrOfUnits, plotDensity, readDataFrame, verify

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The DChipQuantileNormalization class

Description

Package: aroma.affymetrix
Class DChipQuantileNormalization

Directly known subclasses:

public static class DChipQuantileNormalization
extends QuantileNormalization

This class represents a special QuantileNormalization using smooth-splines.

Usage

DChipQuantileNormalization(..., robust=FALSE)

Arguments

...

Arguments passed to the constructor of QuantileNormalization.

robust

If TRUE, the normalization function is estimated robustly, otherwise not.

Details

This normalization method implements the two-pass algorithm described in Bengtsson et al. (2008).

Fields and Methods

Methods:

	`process`	-

Methods inherited from QuantileNormalization:
findTargetDistributionFile, getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.

The DChipSnpInformation class

Description

Package: aroma.affymetrix
Class DChipSnpInformation

Directly known subclasses:

public abstract static class DChipSnpInformation
extends SnpInformation

This class represents dChip genome information files, which typically contains information on nucleotide sequences and fragment lengths of the units.

Usage

DChipSnpInformation(...)

Arguments

...

Arguments passed to SnpInformation.

Details

The dChip SNP information files for various chip types can be downloaded from https://sites.google.com/site/dchipsoft/. Put each file in a directory named identically as the corresponding chip type under the annotations/ directory, e.g. annotations/Mapping50K_Hind240/50k hind snp info AfAm june 05 hg17.xls. Note that dChip changes the filename and file format slightly between chip types, but currently the *byChipType() basically searches for files with names consisting of "snp info" or "snp_info". At least for the most common chip types, there is no need to rename the files in order for this class to recognize them.

Fields and Methods

Methods:

	`byChipType`	-
	`readDataFrame`	-

Methods inherited from SnpInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getData, getFields, getFragmentLengths, getFragmentStarts, getFragmentStops, isCompatibleWithCdf, nbrOfEnzymes, nbrOfUnits, readDataFrame, verify

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The ExonChipEffectFile class

Description

Package: aroma.affymetrix
Class ExonChipEffectFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ExonChipEffectFile

Directly known subclasses:

public abstract static class ExonChipEffectFile
extends ChipEffectFile

This class represents estimates of chip effects in the probe-level models.

Usage

ExonChipEffectFile(..., mergeGroups=FALSE)

Arguments

...

Arguments passed to ChipEffectFile.

mergeGroups

Specifies if the groups are merged or not for these estimates.

Fields and Methods

Methods:

	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The ExonChipEffectSet class

Description

Package: aroma.affymetrix
Class ExonChipEffectSet

Directly known subclasses:

public static class ExonChipEffectSet
extends ChipEffectSet

This class represents estimates of chip effects in the probe-level models.

Usage

ExonChipEffectSet(..., mergeGroups=TRUE)

Arguments

...

Arguments passed to ChipEffectSet.

mergeGroups

Specifies if groups (individual exons in a CDF file) are merged or not for these estimates, i.e. whether transcript-level expression is to be estimated.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getAverageFile`	-
	`getMergeGroups`	-
	`setMergeGroups`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson, Henrik Bengtsson

The ExonProbeAffinityFile class

Description

Package: aroma.affymetrix
Class ExonProbeAffinityFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ExonProbeAffinityFile

Directly known subclasses:

public abstract static class ExonProbeAffinityFile
extends ProbeAffinityFile

This class represents estimates of probe affinities in exon array probe-level models.

Usage

ExonProbeAffinityFile(..., mergeGroups=FALSE)

Arguments

...

Arguments passed to ProbeAffinityFile.

mergeGroups

Specifies if the groups (exons) are merged or not for these estimates.

Fields and Methods

Methods:
No methods defined.

Methods inherited from ProbeAffinityFile:
as.character, getCellIndices, getParameters, readUnits

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The ExonRmaPlm class

Description

Package: aroma.affymetrix
Class ExonRmaPlm

Directly known subclasses:

public abstract static class ExonRmaPlm
extends RmaPlm

This class represents the log-additive model part of the Robust Multichip Analysis (RMA) method described in Irizarry et al (2003), as implemented for exon arrays. The model may be fitted with exons merged into transcripts (all probes fitted together) or on an individual exon basis (probes within an exon treated as a group, but exons fitted separately).

Usage

ExonRmaPlm(..., mergeGroups=TRUE)

Arguments

...

Arguments passed to RmaPlm.

mergeGroups

A logical flag specifying whether to merge exons into transcripts.

Fields and Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getProbeAffinityFile`	-
	`setMergeGroups`	-

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

RmaPlm.

Author(s)

Ken Simpson, Henrik Bengtsson, Elizabeth Purdom

References

Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

The FirmaFile class

Description

Package: aroma.affymetrix
Class FirmaFile

Directly known subclasses:

public abstract static class FirmaFile
extends ParameterCelFile

This class represents scores calculated by the FIRMA algorithm.

Usage

FirmaFile(...)

Arguments

...

Arguments passed to AffymetrixCelFile.

Fields and Methods

Methods:

	`extractMatrix`	-
	`findUnitsTodo`	-
	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The FirmaModel class

Description

Package: aroma.affymetrix
Class FirmaModel

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FirmaModel

Directly known subclasses:

public abstract static class FirmaModel
extends UnitModel

This class represents the FIRMA (Finding Isoforms using RMA) alternative splicing model.

Usage

FirmaModel(rmaPlm=NULL, summaryMethod=c("median", "upperQuartile", "max"),
  operateOn=c("residuals", "weights"), ...)

Arguments

rmaPlm

An @RmaPlm object.

summaryMethod

A character specifying what summarization method should be used.

operateOn

A character specifying what statistic to operate on.

...

Arguments passed to constructor of UnitModel.

Fields and Methods

Methods:

	`fit`	-
	`getCdf`	-
	`getDataSet`	-
	`getFirmaSet`	-
	`getName`	-
	`getPlm`	-
	`getTags`	-

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson, Henrik Bengtsson

The FirmaSet class

Description

Package: aroma.affymetrix
Class FirmaSet

Directly known subclasses:

public static class FirmaSet
extends ParameterCelSet

Usage

FirmaSet(...)

Arguments

...

Arguments passed to constructor of AffymetrixCelSet.

Fields and Methods

Methods:

	`extractMatrix`	-
	`findUnitsTodo`	-
	`getCellIndices`	-
	`readUnits`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson, Henrik Bengtsson

The FragmentEquivalentClassNormalization class

Description

Package: aroma.affymetrix
Class FragmentEquivalentClassNormalization

Directly known subclasses:

public static class FragmentEquivalentClassNormalization
extends ChipEffectTransform

This class represents a normalization method that corrects for systematic effects between loci of different equivalent classes of pairs of sequences that are recognized by the restriction enzymes that cut the DNA studies.

Usage

FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL,
  subsetToFit="-XY")

Arguments

dataSet

A CnChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

targetAvgs

An optional list of functions. For each enzyme there is one target averages to which all arrays should be normalized to.

subsetToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

Fields and Methods

Methods:

	`getAromaUfcFile`	-
	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires an UFC (Unit Fragment Class) annotation file.

Acknowledgments

The idea of normalization signals stratified on enzyme recognition sequences is credited to Jim Veitch and Ben Bolstad at Affymetrix Inc. (2008) who have designed a similar method for copy number estimation in the Affymetrix' Genotype Console v2.

Author(s)

Henrik Bengtsson

The FragmentLengthNormalization class

Description

Package: aroma.affymetrix
Class FragmentLengthNormalization

Directly known subclasses:

public static class FragmentLengthNormalization
extends ChipEffectTransform

This class represents a normalization method that corrects for PCR fragment length effects on copy-number chip-effect estimates.

Usage

FragmentLengthNormalization(dataSet=NULL, ..., target=targetFunctions, subsetToFit="-XY",
  lengthRange=NULL, onMissing=c("median", "ignore"), shift=0, targetFunctions=NULL)

Arguments

dataSet

A SnpChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

target

(Optional) A character string or a list of functions specifying what to normalize toward. For each enzyme there is one target function to which all arrays should be normalized to.

subsetToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

lengthRange

If given, a numeric vector of length 2 specifying the range of fragment lengths considered. All fragments with lengths outside this range are treated as if they were missing.

onMissing

Specifies how to normalize units for which the fragment lengths are unknown.

shift

An optional amount the data points should be shifted (translated).

targetFunctions

Deprecated.

Details

For SNPs, the normalization function is estimated based on the total chip effects, i.e. the sum of the allele signals. The normalizing is done by rescale the chip effects on the intensity scale such that the mean of the total chip effects are the same across samples for any given fragment length. For allele-specific estimates, both alleles are always rescaled by the same amount. Thus, when normalizing allele-specific chip effects, the total chip effects is change, but not the relative allele signal, e.g. the allele B frequency.

Fields and Methods

Methods:

	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires a SNP information annotation file for the chip type to be normalized.

Author(s)

Henrik Bengtsson

The GcContentNormalization class

Description

Package: aroma.affymetrix
Class GcContentNormalization

Directly known subclasses:

public static class GcContentNormalization
extends ChipEffectTransform

Usage

GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)

Arguments

dataSet

A CnChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

targetFunction

A function. The target function to which all arrays should be normalized to.

subsetToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

Fields and Methods

Methods:

	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires an Aroma unit GC-content (UGC) file.

Author(s)

Henrik Bengtsson

The GcContentNormalization2 class

Description

Package: aroma.affymetrix
Class GcContentNormalization2

Directly known subclasses:

public static class GcContentNormalization2
extends AdditiveCovariatesNormalization

This class represents a normalization method that corrects for annotation-data covariate effects on copy-number chip-effect estimates.

Usage

GcContentNormalization2(...)

Arguments

...

Arguments passed to the constructor of AdditiveCovariatesNormalization.

Fields and Methods

Methods:

	`plotCovariateEffects`	-

Methods inherited from AdditiveCovariatesNormalization:
getAsteriskTags, getCdf, getCovariates, getOutputDataSet00, getParameters, process

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The GcRmaBackgroundCorrection class

Description

Package: aroma.affymetrix
Class GcRmaBackgroundCorrection

Directly known subclasses:

public static class GcRmaBackgroundCorrection
extends BackgroundCorrection

This class represents the GCRMA background adjustment function.

Usage

GcRmaBackgroundCorrection(..., indicesNegativeControl=NULL, affinities=NULL,
  type=c("fullmodel", "affinities"), opticalAdjust=TRUE, gsbAdjust=TRUE,
  gsbParameters=NULL, seed=NULL)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

indicesNegativeControl

Locations of any negative control probes (e.g., the anti-genomic controls on the human exon array). If NULL and type == "affinities", then all non-PM probes are used as the negative controls.

affinities

A numeric vector of probe affinities, usually as calculated by computeAffinities() of the AffymetrixCdfFile class.

type

Type (flavor) of background correction, which can be either "fullmodel" (uses MMs; requires that the chip type has PM/MM pairs) or "affinities" (uses probe sequence only).

gsbAdjust

If TRUE, adjustment for specific binding is done, otherwise not.

opticalAdjust

If TRUE, correction for optical effect is done first, utilizing OpticalBackgroundCorrection.

gsbParameters

Additional argument passed to the internal bgAdjustGcrma() method.

seed

An (optional) integer specifying a temporary random seed to be used during processing. The random seed is set to its original state when done. If NULL, it is not set.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson, Henrik Bengtsson

References

[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer. A Model Based Background Adjustment for Oligonucleotide Expression Arrays, JASA, 2004.

The GenericReporter class

Description

Package: aroma.affymetrix
Class GenericReporter

Object
~~|
~~+--GenericReporter

Directly known subclasses:
AffymetrixCelSetReporter, AffymetrixFileSetReporter, SpatialReporter

public abstract static class GenericReporter
extends Object

Usage

GenericReporter(tags="*", ...)

Arguments

tags

A character vector of tags to be added to the output path.

...

Not used.

Fields and Methods

Methods:

	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getTags`	-
	`process`	-
	`setup`	-

Author(s)

Henrik Bengtsson

The GenomeInformation class

Description

Package: aroma.affymetrix
Class GenomeInformation

Directly known subclasses:
AffymetrixCsvGenomeInformation, DChipGenomeInformation, UgpGenomeInformation

public abstract static class GenomeInformation
extends FileCacheKeyInterface

Usage

GenomeInformation(..., .verify=TRUE)

Arguments

...

Arguments passed to GenericDataFile.

.verify

For internal use only.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getChromosomeStats`	-
	`getChromosomes`	-
	`getData`	-
	`getPositions`	-
	`getUnitsOnChromosome`	-
	`getUnitsOnChromosomes`	-
	`nbrOfUnits`	-
	`plotDensity`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

Static method to define a genome information set by chip type

Description

Static method to define a genome information set by chip type.

Usage

## Static method (use this):
## GenomeInformation$byChipType()

## Don't use the below:
## S3 method for class 'GenomeInformation'
byChipType(...)

Arguments

...

Not used.

Value

Returns a GenomeInformation object.

Static method to define a genome information set from a CDF

Description

Static method to define a genome information set from a CDF.

Usage

## Static method (use this):
## GenomeInformation$fromCdf(cdf, ...)

## Don't use the below:
## S3 method for class 'GenomeInformation'
fromCdf(static, cdf, ...)

Arguments

cdf

An AffymetrixCdfFile.

...

Additional argument passed to *byChipType().

Value

Returns a GenomeInformation object.

The HetLogAddCnPlm class

Description

Package: aroma.affymetrix
Class HetLogAddCnPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--HetLogAddPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--HetLogAddSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--HetLogAddCnPlm

Directly known subclasses:

public abstract static class HetLogAddCnPlm
extends CnPlm

Usage

HetLogAddCnPlm(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to HetLogAddCnPlm.

combineAlleles

If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from HetLogAddSnpPlm:
getAsteriskTags

Methods inherited from HetLogAddPlm:
getAsteriskTags, getFitUnitGroupFunction

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

TO DO.

Author(s)

Henrik Bengtsson

The HetLogAddPlm class

Description

Package: aroma.affymetrix
Class HetLogAddPlm

Directly known subclasses:
HetLogAddCnPlm, HetLogAddSnpPlm

public abstract static class HetLogAddPlm
extends RmaPlm

This class represents a log-additive model similar to the one described in Irizarry et al (2003), except that the errors may have different variances for different probes.

Usage

HetLogAddPlm(...)

Arguments

...

Arguments passed to RmaPlm.

Fields and Methods

Methods:
No methods defined.

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The HetLogAddSnpPlm class

Description

Package: aroma.affymetrix
Class HetLogAddSnpPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--HetLogAddPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--HetLogAddSnpPlm

Directly known subclasses:
HetLogAddCnPlm

public abstract static class HetLogAddSnpPlm
extends SnpPlm

Usage

HetLogAddSnpPlm(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to HetLogAddPlm.

mergeStrands

If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from HetLogAddPlm:
getAsteriskTags, getFitUnitGroupFunction

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The LimmaBackgroundCorrection class

Description

Package: aroma.affymetrix
Class LimmaBackgroundCorrection

Directly known subclasses:
NormExpBackgroundCorrection

public static class LimmaBackgroundCorrection
extends BackgroundCorrection

This class represents the various "background" correction methods implemented in the limma package.

Usage

LimmaBackgroundCorrection(..., args=NULL, addJitter=FALSE, jitterSd=0.2, seed=6022007)

Arguments

...

Arguments passed to the constructor of BackgroundCorrection.

args

A list of additional arguments passed to the correction algorithm.

addJitter

If TRUE, Zero-mean gaussian noise is added to the signals before being background corrected.

jitterSd

Standard deviation of the jitter noise added.

seed

An (optional) integer specifying a temporary random seed to be used for generating the (optional) jitter. The random seed is set to its original state when done. If NULL, it is not set.

Details

By default, only PM signals are background corrected and MMs are left unchanged.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Jitter noise

The fitting algorithm of the normal+exponential background correction model may not converge if there too many small and discrete signals. To overcome this problem, a small amount of noise may be added to the signals before fitting the model. This is an ad hoc solution that seems to work. However, adding Gaussian noise may generate non-positive signals.

Author(s)

Henrik Bengtsson. Adopted from RmaBackgroundCorrection by Ken Simpson.

The LinearModelProbeSequenceNormalization class

Description

Package: aroma.affymetrix
Class LinearModelProbeSequenceNormalization

Directly known subclasses:
BasePositionNormalization

public abstract static class LinearModelProbeSequenceNormalization
extends AbstractProbeSequenceNormalization

This abstract class represents a normalization method that corrects for systematic effects in the probe intensities due to probe-sequence dependent effects that can be modeled using a linear model.

Usage

LinearModelProbeSequenceNormalization(...)

Arguments

...

Arguments passed to the constructor of AbstractProbeSequenceNormalization.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires that an aroma probe sequence file is available for the chip type.

Memory usage

The model fitting methods of this class are bounded in memory. This is done by first building up the normal equations incrementally in chunks of cells. The generation of normal equations is otherwise the step that consumes the most memory. When the normal equations are available, the solve() method is used to solve the equations. Note that this algorithm is still exact.

Author(s)

Henrik Bengtsson

The MatNormalization class

Description

Package: aroma.affymetrix
Class MatNormalization

Directly known subclasses:

public static class MatNormalization
extends AbstractProbeSequenceNormalization

This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in the number of A, C, G, and T:s and the match scores according to MAT [1].

Usage

MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)

Arguments

...

Arguments passed to the constructor of AbstractProbeSequenceNormalization.

unitsToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

model

A character string specifying the model used to fit the base-count effects.

nbrOfBins

The number of bins to use for the variance smoothing step.

Fields and Methods

Methods:

	`process`	-

Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires that an aroma probe sequence file and aroma match scores file is available for the chip type.

Author(s)

Mark Robinson

References

[1] Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip, PNAS, 2006.

The MatSmoothing class

Description

Package: aroma.affymetrix
Class MatSmoothing

Directly known subclasses:

public static class MatSmoothing
extends ProbeLevelTransform

This class represents a function for smoothing data with a trimmed mean.

Usage

MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)

Arguments

...

Arguments passed to ProbeLevelTransform.

design

A design matrix.

probeWindow

Bandwidth to use. Effectively the width is 2*probeWindow since it looks probeWindow bases in either direction.

nProbes

The minimum number of probes to calculate a MAT score for.

meanTrim

The amount of trimming of the mean in [0,0.5].

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Mark Robinson, Henrik Bengtsson

The MbeiCnPlm class

Description

Package: aroma.affymetrix
Class MbeiCnPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--MbeiPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--MbeiSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--MbeiCnPlm

Directly known subclasses:

public abstract static class MbeiCnPlm
extends CnPlm

Usage

MbeiCnPlm(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to MbeiSnpPlm.

combineAlleles

If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from MbeiSnpPlm:
getAsteriskTags

Methods inherited from MbeiPlm:
getAsteriskTags, getFitUnitGroupFunction

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The MbeiPlm class

Description

Package: aroma.affymetrix
Class MbeiPlm

Directly known subclasses:
MbeiCnPlm, MbeiSnpPlm

public abstract static class MbeiPlm
extends ProbeLevelModel

This class represents the model-based expression indexes (MBEI) multiplicative model in Li & Wong (2001).

Usage

MbeiPlm(...)

Arguments

...

Arguments passed to ProbeLevelModel.

Fields and Methods

Methods:
No methods defined.

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

For a single unit group, the multiplicative model is:

y_{ik} = \theta_i \phi_k + \varepsilon_{ik}

where \theta_i are the chip effects for arrays i=1,...,I, and \phi_k are the probe affinities for probes k=1,...,K. The \varepsilon_{ik} are zero-mean noise with equal variance. To make to parameters identifiable, the constraint \prod_k \phi_k = 1 is added.

Author(s)

Henrik Bengtsson

References

Li, C. and Wong, W.H. (2001), Genome Biology 2, 1-11.
Li, C. and Wong, W.H. (2001), Proc. Natl. Acad. Sci USA 98, 31-36.

The MbeiSnpPlm class

Description

Package: aroma.affymetrix
Class MbeiSnpPlm

Directly known subclasses:
MbeiCnPlm

public abstract static class MbeiSnpPlm
extends SnpPlm

Usage

MbeiSnpPlm(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to MbeiPlm.

mergeStrands

If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from MbeiPlm:
getAsteriskTags, getFitUnitGroupFunction

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The Model class

Description

Package: aroma.affymetrix
Class Model

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model

Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AlleleSummation, AvgCnPlm, AvgPlm, AvgSnpPlm, CrlmmModel, ExonRmaPlm, FirmaModel, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, MultiArrayUnitModel, ProbeLevelModel, RmaCnPlm, RmaPlm, RmaSnpPlm, SingleArrayUnitModel, UnitModel

public abstract static class Model
extends ParametersInterface

This class is abstract and represents a generic model that applies to a data set.

Usage

Model(dataSet=NULL, tags="*", ..., .onUnknownArgs=c("error", "warning", "ignore"))

Arguments

dataSet

The data set to which this model should be fitted.

tags

A character vector of tags to be appended to the tags of the input data set.

...

Not used.

.onUnknownArgs

A character string specifying what should occur if there are unknown arguments in ....

Fields and Methods

Methods:

	`fit`	-
	`getAsteriskTags`	-
	`getDataSet`	-
	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getTags`	-
	`setTags`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The MultiArrayUnitModel class

Description

Package: aroma.affymetrix
Class MultiArrayUnitModel

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel

Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, ProbeLevelModel, RmaCnPlm, RmaPlm, RmaSnpPlm

public abstract static class MultiArrayUnitModel
extends UnitModel

This abstract class represents a unit model that fits one model per unit based on signals for all arrays in the data set. The nature of a multi-array unit model is that all arrays must be available at the time of the fit and the estimated parameters will depend on the data from all arrays. Thus, if the signals in one array changes the model has to be refitted.

Usage

MultiArrayUnitModel(..., listOfPriors=NULL)

Arguments

...

Arguments passed to UnitModel.

listOfPriors

A list of priors to be used when fitting the model.

Fields and Methods

Methods:

	`getListOfPriors`	-
	`setListOfPriors`	-

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

Static method to get the low-level function that fits the PLM

Description

Static method to get the low-level function that fits the PLM. Any subclass model must provide this method, which should return a function that accepts an IxK matrix.

Usage

## Static method (use this):
## MultiArrayUnitModel$getFitUnitGroupFunction()

## Don't use the below:
## S3 method for class 'MultiArrayUnitModel'
getFitUnitGroupFunction(...)

Arguments

...

Not used.

Value

Returns a function.

Non-documented objects

Description

This page contains aliases for all "non-documented" objects that R CMD check detects in this package.

Almost all of them are generic functions that have specific document for the corresponding method coupled to a specific class. Other functions are re-defined by setMethodS3() to default methods. Neither of these two classes are non-documented in reality. The rest are deprecated methods.

The NormExpBackgroundCorrection class

Description

Package: aroma.affymetrix
Class NormExpBackgroundCorrection

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--LimmaBackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--NormExpBackgroundCorrection

Directly known subclasses:

public static class NormExpBackgroundCorrection
extends LimmaBackgroundCorrection

This class represents the normal exponential background correction model. Estimators of the limma package is used.

Usage

NormExpBackgroundCorrection(..., method=c("rma", "saddle", "mle"))

Arguments

...

Arguments passed to the constructor of LimmaBackgroundCorrection.

method

The estimator used, cf. argument normexp.method of backgroundCorrect in limma for more details.

Fields and Methods

Methods:
No methods defined.

Methods inherited from LimmaBackgroundCorrection:
getAsteriskTags, getParameters, process

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The OpticalBackgroundCorrection class

Description

Package: aroma.affymetrix
Class OpticalBackgroundCorrection

Directly known subclasses:

public static class OpticalBackgroundCorrection
extends BackgroundCorrection

This class represents "optical" background adjustment.

Usage

OpticalBackgroundCorrection(..., minimum=1)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

minimum

The minimum signal allowed after adjustment.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson

The ParameterCelFile class

Description

Package: aroma.affymetrix
Class ParameterCelFile

Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ProbeAffinityFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile

public abstract static class ParameterCelFile
extends ParametersInterface

A ParameterCelFile object represents parameter estimates.

Usage

ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)

Arguments

...

Arguments passed to AffymetrixCelFile.

encodeFunction

A function taking a single list structure as its argument.

decodeFunction

A function taking a single list structure as its argument.

Fields and Methods

Methods:

	`extractDataFrame`	-
	`extractMatrix`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

File format

The idea behind this class is store data fields which by nature have one value per probe (per field) in CEL files. A perfect example is to store probe-affinity estimates and their standard deviations. There is one probe affinity per probe so the structure of a CEL file (and its coupled CDF file) is well suited to read/write such information.

Consider a unit group with L probes. A CEL file stores intensities (L floats), stdvs (L floats), and pixels (L integers). Thus, for each probe l=1,...,L, a (float, float, integer) tuple is stored. We can use this for any information we want. If we want a slightly different structure, we can choose to encode/decode our structure/information to fit the structure of the CEL file. This abstract class provides transparent methods for encoding and decoding such information through methods encodeUnitGroup() and decodeUnitGroup(). By subclassing you can implement different types of data structures.

Author(s)

Henrik Bengtsson

The ParameterCelSet class

Description

Package: aroma.affymetrix
Class ParameterCelSet

Directly known subclasses:
ChipEffectSet, CnChipEffectSet, ExonChipEffectSet, FirmaSet, SnpChipEffectSet

public static class ParameterCelSet
extends ParametersInterface

A ParameterCelSet object represents a set of ParameterCelFile:s.

Usage

ParameterCelSet(...)

Arguments

...

Arguments passed to AffymetrixCelSet.

Fields and Methods

Methods:

	`extractDataFrame`	-
	`extractMatrix`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The ProbeAffinityFile class

Description

Package: aroma.affymetrix
Class ProbeAffinityFile

Directly known subclasses:
CnProbeAffinityFile, ExonProbeAffinityFile, SnpProbeAffinityFile

public abstract static class ProbeAffinityFile
extends ParameterCelFile

This class represents estimates of probe affinities in probe-level models.

Usage

ProbeAffinityFile(..., probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm"))

Arguments

...

Arguments passed to ParameterCelFile.

probeModel

The specific type of probe model.

Fields and Methods

Methods:

	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The ProbeLevelModel class

Description

Package: aroma.affymetrix
Class ProbeLevelModel

public abstract static class ProbeLevelModel
extends MultiArrayUnitModel

This abstract class represents a probe-level model (PLM) as defined by the affyPLM package: "A [...] PLM is a model that is fit to probe-intensity data. More specifically, it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis", where the more general case for a probeset is a unit group in Affymetrix CDF terms.

Usage

ProbeLevelModel(..., standardize=TRUE)

Arguments

...

Arguments passed to MultiArrayUnitModel.

standardize

If TRUE, chip-effect and probe-affinity estimates are rescaled such that the product of the probe affinities is one.

Details

In order to minimize the risk for mistakes, but also to be able compare results from different PLMs, all PLM subclasses must meet the following criteria:

All parameter estimates must be (stored and returned) on the intensity scale, e.g. log-additive models such as RmaPlm have to transform the parameters on the log-scale to the intensity scale.
The probe-affinity estimates \phi_k for a unit group must be constrained such that \prod_k \phi_k = 1, or equivalently if \phi_k > 0,\sum_k \log(\phi_k) = 0.

Note that the above probe-affinity constraint guarantees that the estimated chip effects across models are on the same scale.

Fields and Methods

Methods:

	`fit`	-
	`getChipEffectSet`	-
	`getProbeAffinityFile`	-
	`getResidualSet`	-
	`getWeightsSet`	-

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ProbeLevelTransform class

Description

Package: aroma.affymetrix
Class ProbeLevelTransform

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform

Directly known subclasses:
AbstractProbeSequenceNormalization, AllelicCrosstalkCalibration, BackgroundCorrection, BaseCountNormalization, BasePositionNormalization, DChipQuantileNormalization, GcRmaBackgroundCorrection, LimmaBackgroundCorrection, LinearModelProbeSequenceNormalization, MatNormalization, MatSmoothing, NormExpBackgroundCorrection, OpticalBackgroundCorrection, ProbeLevelTransform3, QuantileNormalization, ReseqCrosstalkCalibration, RmaBackgroundCorrection, ScaleNormalization, ScaleNormalization3, SpatialRowColumnNormalization, UnitTypeScaleNormalization

public abstract static class ProbeLevelTransform
extends Transform

This abstract class represents a transformation methods that transforms probe-level signals, typically intensities.

Usage

ProbeLevelTransform(...)

Arguments

...

Arguments passed to the constructor of Transform.

Details

Subclasses must implement the process() method.

Fields and Methods

Methods:
No methods defined.

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ProbeLevelTransform3 class

Description

Package: aroma.affymetrix
Class ProbeLevelTransform3

Directly known subclasses:
AbstractProbeSequenceNormalization, BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization, ScaleNormalization3, UnitTypeScaleNormalization

public abstract static class ProbeLevelTransform3
extends ProbeLevelTransform

This abstract class is specialized from ProbeLevelTransform and provides methods to identify subsets and types of probes that are used for fitting and/or updating the signals.

Usage

ProbeLevelTransform3(dataSet=NULL, ..., unitsToFit="-XY", typesToFit=typesToUpdate,
  unitsToUpdate=NULL, typesToUpdate="pm", shift=0)

Arguments

dataSet

A AffymetrixCelSet.

...

Arguments passed to the constructor of ProbeLevelTransform.

unitsToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

typesToFit

Types of probes to be used when fitting the model.

unitsToUpdate

The units to be updated. If NULL, all are considered.

typesToUpdate

Types of probes to be updated.

shift

An optional amount to shift data before fitting and updating.

Fields and Methods

Methods:
No methods defined.

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The QualityAssessmentFile class

Description

Package: aroma.affymetrix
Class QualityAssessmentFile

Directly known subclasses:

public abstract static class QualityAssessmentFile
extends AffymetrixCelFile

This class represents probe-level QC information (residuals, weights, etc.)

Usage

QualityAssessmentFile(...)

Arguments

...

Arguments passed to AffymetrixCelFile.

Fields and Methods

Methods:

	`findUnitsTodo`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson

The QualityAssessmentModel class

Description

Package: aroma.affymetrix
Class QualityAssessmentModel

Object
~~|
~~+--QualityAssessmentModel

Directly known subclasses:

public static class QualityAssessmentModel
extends Object

Usage

QualityAssessmentModel(plm=NULL, tags="*", ...)

Arguments

plm

A ProbeLevelModel.

tags

A character vector of tags.

...

Not used.

Fields and Methods

Methods:

	`getChipEffectSet`	-
	`getDataSet`	-
	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getPlm`	-
	`getResiduals`	-
	`getTags`	-
	`getWeights`	-
	`nbrOfArrays`	-
	`plotNuse`	-
	`plotRle`	-

Author(s)

Ken Simpson, Henrik Bengtsson

The QualityAssessmentSet class

Description

Package: aroma.affymetrix
Class QualityAssessmentSet

Directly known subclasses:

public static class QualityAssessmentSet
extends AffymetrixCelSet

Usage

QualityAssessmentSet(...)

Arguments

...

Arguments passed to constructor of AffymetrixCelSet.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson

The QuantileNormalization class

Description

Package: aroma.affymetrix
Class QuantileNormalization

Directly known subclasses:
DChipQuantileNormalization

public static class QuantileNormalization
extends ProbeLevelTransform

This class represents a normalization function that transforms the probe-level signals towards the same empirical distribution.

Usage

QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL,
  targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

subsetToUpdate

The probes to be updated. If NULL, all probes are updated.

typesToUpdate

Types of probes to be updated.

targetDistribution

A numeric vector. The empirical distribution to which all arrays should be normalized to.

subsetToAvg

The probes to calculate average empirical distribution over. If a single numeric in (0,1), then this fraction of all probes will be used. If NULL, all probes are considered.

typesToAvg

Types of probes to be used when calculating the average empirical distribution. If "pm" and "mm" only perfect-match and mismatch probes are used, respectively. If "pmmm" both types are used.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

Examples

## Not run: 
  for (zzz in 0) {

# Setup verbose output
verbose <- Arguments$getVerbose(-2)
timestampOn(verbose)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define an example dataset
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Find any dataset
path <- NULL
if (is.null(path))
  break

ds <- AffymetrixCelSet$fromFiles(path)
print(ds)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Normalization
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
norm <- QuantileNormalization(ds, subsetToAvg=1/3)
dsQN <- process(norm, verbose=verbose)
print(dsQN)

} # for (zzz in 0)
rm(zzz)


## End(Not run)

The ReseqCrosstalkCalibration class

Description

Package: aroma.affymetrix
Class ReseqCrosstalkCalibration

Directly known subclasses:

public static class ReseqCrosstalkCalibration
extends ProbeLevelTransform

This class represents a calibration function that transforms the probe-level signals such that the signals from the four nucleotides (A, C, G, T) are orthogonal.

Usage

ReseqCrosstalkCalibration(dataSet=NULL, ..., targetAvg=2200, subsetToAvg=NULL,
  mergeGroups=FALSE, flavor=c("sfit", "expectile"), alpha=c(0.1, 0.075, 0.05, 0.03,
  0.01), q=2, Q=98)

Arguments

dataSet

An AffymetrixCelSet.

...

Arguments passed to the constructor of ProbeLevelTransform.

targetAvg

The signal(s) that the average of the sum of the probe quartets should have after calibration.

subsetToAvg

The indices of the cells (taken as the intersect of existing indices) used to calculate average in order to rescale to the target average. If NULL, all probes are considered.

mergeGroups

A logical ...

flavor

A character string specifying what algorithm is used to fit the crosstalk calibration.

alpha, q, Q

Additional arguments passed to fitMultiDimensionalCone().

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ResidualFile class

Description

Package: aroma.affymetrix
Class ResidualFile

Directly known subclasses:

public abstract static class ResidualFile
extends ParameterCelFile

This class represents estimates of residuals in the probe-level models.

Usage

ResidualFile(..., probeModel=c("pm"))

Arguments

...

Arguments passed to ParameterCelFile.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getImage`	-
	`readUnits`	-
	`writeImage`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The ResidualSet class

Description

Package: aroma.affymetrix
Class ResidualSet

Directly known subclasses:

public static class ResidualSet
extends ParametersInterface

This class represents probe-level residuals from probe-level models.

Usage

ResidualSet(..., probeModel=c("pm"))

Arguments

...

Arguments passed to AffymetrixCelSet.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getAverageFile`	-
	`getCellIndices`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson, Henrik Bengtsson

The RmaBackgroundCorrection class

Description

Package: aroma.affymetrix
Class RmaBackgroundCorrection

Directly known subclasses:

public static class RmaBackgroundCorrection
extends BackgroundCorrection

This class represents the RMA background adjustment function.

Usage

RmaBackgroundCorrection(..., addJitter=FALSE, jitterSd=0.2, seed=6022007)

Arguments

...

Arguments passed to the constructor of BackgroundCorrection.

addJitter

If TRUE, Zero-mean gaussian noise is added to the signals before being background corrected.

jitterSd

Standard deviation of the jitter noise added.

seed

An (optional) integer specifying a temporary random seed to be used for generating the (optional) jitter. The random seed is set to its original state when done. If NULL, it is not set.

Details

Internally bg.adjust is used to background correct the probe signals. The default is to background correct PM signals only.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Jitter noise

The fitting algorithm of the RMA background correction model may not converge if there too many small and discrete signals. To overcome this problem, a small amount of noise may be added to the signals before fitting the model. This is an ad hoc solution that seems to work. However, add Gaussian noise may generate non-positive signals.

Author(s)

Ken Simpson, Henrik Bengtsson

The RmaCnPlm class

Description

Package: aroma.affymetrix
Class RmaCnPlm

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaCnPlm

Directly known subclasses:

public abstract static class RmaCnPlm
extends CnPlm

Usage

RmaCnPlm(..., combineAlleles=FALSE)

Arguments

...

Arguments passed to RmaSnpPlm.

combineAlleles

If FALSE, allele A and allele B are treated separately, otherwise together.

Fields and Methods

Methods:
No methods defined.

Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from RmaSnpPlm:
getAsteriskTags

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

TO DO.

Author(s)

Henrik Bengtsson

The RmaPlm class

Description

Package: aroma.affymetrix
Class RmaPlm

Directly known subclasses:
ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, RmaCnPlm, RmaSnpPlm

public abstract static class RmaPlm
extends ProbeLevelModel

This class represents the log-additive model part of the Robust Multichip Analysis (RMA) method described in Irizarry et al (2003).

Usage

RmaPlm(..., flavor=c("affyPLM", "oligo"))

Arguments

...

Arguments passed to ProbeLevelModel.

flavor

A character string specifying what model fitting algorithm to be used. This makes it possible to get identical estimates as other packages.

Fields and Methods

Methods:
No methods defined.

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Model

For a single unit group, the log-additive model of RMA is:

log_2(y_{ik}) = \beta_i + \alpha_k + \varepsilon_{ik}

where \beta_i are the chip effects for arrays i=1,...,I, and \alpha_k are the probe affinities for probes k=1,...,K. The \varepsilon_{ik} are zero-mean noise with equal variance. The model is constrained such that \sum_k{\alpha_k} = 0.

Note that all PLM classes must return parameters on the intensity scale. For this class that means that \theta_i = 2^\beta_i and \phi_k = 2^\alpha_k are returned.

Different flavors of model fitting

There are a few differ algorithms available for fitting the same probe-level model. The default and recommended method (flavor="affyPLM") uses the implementation in the preprocessCore package which fits the model parameters robustly using an M-estimator (the method used to be in affyPLM).

Alternatively, other model-fitting algorithms are available. The algorithm (flavor="oligo") used by the oligo package, which originates from the affy packages, fits the model using median polish, which is a non-robust estimator. Note that this algorithm does not constraint the probe-effect parameters to multiply to one on the intensity scale. Since the internal function does not return these estimates, we can neither rescale them.

Author(s)

Henrik Bengtsson, Ken Simpson

References

Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

The RmaSnpPlm class

Description

Package: aroma.affymetrix
Class RmaSnpPlm

Directly known subclasses:
RmaCnPlm

public abstract static class RmaSnpPlm
extends SnpPlm

Usage

RmaSnpPlm(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to RmaPlm.

mergeStrands

If TRUE, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ScaleNormalization class

Description

Package: aroma.affymetrix
Class ScaleNormalization

Directly known subclasses:

public static class ScaleNormalization
extends ProbeLevelTransform

This class represents a normalization function that transforms the probe-level signals towards the same scale.

Usage

ScaleNormalization(dataSet=NULL, ..., targetAvg=4400, subsetToUpdate=NULL,
  typesToUpdate=NULL, subsetToAvg="-XY", typesToAvg=typesToUpdate, shift=0)

Arguments

dataSet

AffymetrixCelSet to be normalized.

...

Arguments passed to the constructor of ProbeLevelTransform.

targetAvg

A numeric value.

subsetToUpdate

The probes to be updated. If NULL, all probes are updated.

typesToUpdate

Types of probes to be updated.

subsetToAvg

The probes to calculate average signal over. If a single numeric in (0,1), then this fraction of all probes will be used. If NULL, all probes are considered.

typesToAvg

Types of probes to be used when calculating the average signal. If "pm" and "mm" only perfect-match and mismatch probes are used, respectively. If "pmmm" both types are used.

shift

Optional amount of shift if data before fitting/normalizing.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ScaleNormalization3 class

Description

Package: aroma.affymetrix
Class ScaleNormalization3

Directly known subclasses:

public static class ScaleNormalization3
extends ProbeLevelTransform3

This class represents a normalization function that transforms the probe-level signals towards the same scale.

Usage

ScaleNormalization3(..., targetAvg=4400)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform3.

targetAvg

A numeric value.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The SingleArrayUnitModel class

Description

Package: aroma.affymetrix
Class SingleArrayUnitModel

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--SingleArrayUnitModel

Directly known subclasses:

public abstract static class SingleArrayUnitModel
extends UnitModel

This abstract class represents a unit model that fits one model per unit based on signals from a single arrays. The nature of a single-array unit model is that each array can be fitted independently of the others.

Usage

SingleArrayUnitModel(...)

Arguments

...

Arguments passed to UnitModel.

Fields and Methods

Methods:

	`fit`	-

Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

Static method to get the low-level function that fits the PLM

Description

Static method to get the low-level function that fits the PLM. Any subclass model must provide this method, which should return a function that accepts a numeric vector of length K, where K is the number of probes.

Usage

## Static method (use this):
## SingleArrayUnitModel$getFitUnitGroupFunction()

## Don't use the below:
## S3 method for class 'SingleArrayUnitModel'
getFitUnitGroupFunction(...)

Arguments

...

Not used.

Value

Returns a function.

The SmoothMultiarrayModel class

Description

Package: aroma.affymetrix
Class SmoothMultiarrayModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--SmoothMultiarrayModel

Directly known subclasses:
SmoothRmaModel, SmoothSaModel

public abstract static class SmoothMultiarrayModel
extends ChromosomalModel

This abstract class represents a chromosomal smoothing method done chromosome by chromosome.

Usage

SmoothMultiarrayModel(..., typoOfWeights=c("none", "1/s2"), bandwidth=10000, tags="*")

Arguments

...

Arguments passed to the constructor of ChromosomalModel.

typoOfWeights

A character string.

bandwidth

A single numeric specifying the smoothing bandwidth in units of nucleotides.

tags

A character vector of tags to be added.

Fields and Methods

Methods:

	`getBandwidth`	-
	`getOutputTuple`	-
	`setBandwidth`	-

Methods inherited from ChromosomalModel:
as.character, fit, getAlias, getAromaGenomeTextFile, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSetTuple, getSets, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setChromosomes, setGenome, getListOfGenomeInformations, getPcuTheta, getPositionChipTypeUnit

Author(s)

Henrik Bengtsson

The SmoothRmaModel class

Description

Package: aroma.affymetrix
Class SmoothRmaModel

Object
~~|
~~+--ChromosomalModel
~~~~~~~|
~~~~~~~+--SmoothMultiarrayModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--SmoothRmaModel

Directly known subclasses:

public abstract static class SmoothRmaModel
extends SmoothMultiarrayModel

This class represents the Chromosomal Smoothing Robust Multichip Analysis method.

Usage

SmoothRmaModel(...)

Arguments

...

Arguments passed to the constructor of SmoothMultiarrayModel.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SmoothMultiarrayModel:
as.character, createOutputTuple, fitOneChromosome, getAsteriskTags, getBandwidth, getFitUnitGroupFunction, getOutputTuple, getRootPath, setBandwidth

Author(s)

Henrik Bengtsson

The SnpChipEffectFile class

Description

Package: aroma.affymetrix
Class SnpChipEffectFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpChipEffectFile

Directly known subclasses:
CnChipEffectFile

public abstract static class SnpChipEffectFile
extends ChipEffectFile

This class represents estimates of chip effects in the probe-level models.

Usage

SnpChipEffectFile(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to ChipEffectFile.

mergeStrands

Specifies if the strands are merged or not for these estimates.

Fields and Methods

Methods:

	`extractTheta`	-
	`extractTotalAndFracB`	-
	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The SnpChipEffectGroupMerge class

Description

Package: aroma.affymetrix
Class SnpChipEffectGroupMerge

Directly known subclasses:

public static class SnpChipEffectGroupMerge
extends ChipEffectGroupMerge

This class represents a method that merges SNP chip effects across groups unit by unit.

Usage

SnpChipEffectGroupMerge(..., mergeStrands=FALSE, mean=c("arithmetic", "geometric"))

Arguments

...

Arguments passed to the constructor of ChipEffectGroupMerge.

mergeStrands

If TRUE, group strands are merged.

mean

A character string specifying what type of averaging should be applied.

Fields and Methods

Methods:

	`getMergeFunction`	-

Methods inherited from ChipEffectGroupMerge:
getCdf, getMergeFunction, getParameters, process, setMergeFunction

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The SnpChipEffectSet class

Description

Package: aroma.affymetrix
Class SnpChipEffectSet

Directly known subclasses:
CnChipEffectSet

public static class SnpChipEffectSet
extends ChipEffectSet

This class represents estimates of chip effects in the probe-level models.

Usage

SnpChipEffectSet(..., mergeStrands="byFirstFile")

Arguments

...

Arguments passed to ChipEffectSet.

mergeStrands

Specifies if the strands are merged or not for these estimates.

Fields and Methods

Methods:

	`extractAlleleSet`	-
	`extractSnpCnvQSet`	-
	`extractSnpQSet`	-
	`extractTheta`	-
	`extractTotalAndFreqB`	-
	`getAverageFile`	-
	`getMergeStrands`	-
	`setMergeStrands`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The SnpInformation class

Description

Package: aroma.affymetrix
Class SnpInformation

Directly known subclasses:
DChipSnpInformation, UflSnpInformation

public abstract static class SnpInformation
extends FileCacheKeyInterface

Usage

SnpInformation(...)

Arguments

...

Arguments passed to GenericDataFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getData`	-
	`getFragmentLengths`	-
	`getFragmentStarts`	-
	`getFragmentStops`	-
	`nbrOfEnzymes`	-
	`nbrOfUnits`	-
	`readDataFrame`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

Static method to define a genome information set from a CDF

Description

Static method to define a genome information set from a CDF.

Usage

## Static method (use this):
## SnpInformation$fromCdf(cdf, ...)

## Don't use the below:
## S3 method for class 'SnpInformation'
fromCdf(static, cdf, ...)

Arguments

cdf

An AffymetrixCdfFile.

...

Additional argument passed to *byChipType().

Value

Returns a SnpInformation object.

The SnpPlm interface class

Description

Package: aroma.affymetrix
Class SnpPlm

Interface
~~|
~~+--SnpPlm

Directly known subclasses:
AffineCnPlm, AffineSnpPlm, AvgCnPlm, AvgSnpPlm, CnPlm, HetLogAddCnPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiSnpPlm, RmaCnPlm, RmaSnpPlm

public class SnpPlm
extends Interface

An Interface implementing methods special for ProbeLevelModels specific to SNP arrays.

Usage

SnpPlm(...)

Arguments

...

Not used.

Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getMergeStrands`	-
	`getProbeAffinityFile`	-
	`setMergeStrands`	-

Methods inherited from Interface:
extend, print, uses

Requirements

Classes inheriting from this Interface must provide the following fields:

mergeStrands: A logical value indicating if strands should be merged or not.

Author(s)

Henrik Bengtsson

Examples

for (zzz in 0) {

# Setup verbose output
verbose <- Arguments$getVerbose(-2)
timestampOn(verbose)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define an example dataset using this path
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Find any SNP dataset
path <- NULL
if (is.null(path))
  break

if (!exists("ds")) {
  ds <- AffymetrixCelSet$fromFiles(path)
}
print(ds)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Create a set of various PLMs for this dataset
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("models", mode="list")) {
  mergeStrands <- TRUE
  models <- list(
    rma = RmaSnpPlm(ds, mergeStrands=mergeStrands),
    mbei = MbeiSnpPlm(ds, mergeStrands=mergeStrands)
#   affine = AffineSnpPlm(ds, background=FALSE, mergeStrands=mergeStrands)
  )
}
print(models)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# For each model, fit a few units
#
# Note, by fitting the same set of units across models, the internal
# caching mechanisms of aroma.affymetrix makes sure that the data is
# only read into memory once. See log for reading speed.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
units <- 55+1:100

for (model in models) {
  ruler(verbose)
  fit(model, units=units, force=TRUE, verbose=verbose)
}

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# For each unit, plot the estimated (thetaB,thetaA) for all models
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Should we plot the on the log scale?
log <- TRUE

# Do only user to press ENTER if more than one unit is plotted
opar <- par(ask=(length(units) > 1))

Alab <- expression(theta[A])
Blab <- expression(theta[B])
if (log) {
  lim <- c(6, 16)
} else {
  lim <- c(0, 2^15)
}

# For each unit...
for (unit in units) {
  # For all models...
  for (kk in seq_along(models)) {
    ces <- getChipEffects(models[[kk]])
    ceUnit <- ces[unit]
    snpName <- names(ceUnit)[1]
    theta <- ceUnit[[1]]
    thetaA <- theta[[1]]$theta
    thetaB <- theta[[2]]$theta
    if (log) {
      thetaA <- log(thetaA, base=2)
      thetaB <- log(thetaB, base=2)
    }

    # Create the plot?
    if (kk == 1) {
      plot(NA, xlim=lim, ylim=lim, xlab=Blab, ylab=Alab, main=snpName)
      abline(a=0, b=1, lty=2)
    }

    # Plot the estimated parameters
    points(thetaB, thetaA, col=kk, pch=19)
  }
} # for (unit ...)

# Reset graphical parameter settings
par(opar)

} # for (zzz in 0)
rm(zzz)

The SnpProbeAffinityFile class

Description

Package: aroma.affymetrix
Class SnpProbeAffinityFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpProbeAffinityFile

Directly known subclasses:
CnProbeAffinityFile

public abstract static class SnpProbeAffinityFile
extends ProbeAffinityFile

This class represents estimates of probe affinities in SNP probe-level models.

Usage

SnpProbeAffinityFile(..., mergeStrands=FALSE)

Arguments

...

Arguments passed to ProbeAffinityFile.

mergeStrands

Specifies if the strands are merged or not for these estimates.

Fields and Methods

Methods:
No methods defined.

Methods inherited from ProbeAffinityFile:
as.character, getCellIndices, getParameters, readUnits

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The SpatialReporter class

Description

Package: aroma.affymetrix
Class SpatialReporter

Object
~~|
~~+--GenericReporter
~~~~~~~|
~~~~~~~+--AffymetrixFileSetReporter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AffymetrixCelSetReporter
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--SpatialReporter

Directly known subclasses:

public abstract static class SpatialReporter
extends AffymetrixCelSetReporter

A SpatialReporter generates image files of spatial representations of cell signals for each of the arrays in the input set.

Usage

SpatialReporter(..., reference=NULL)

Arguments

...

Arguments passed to AffymetrixCelSetReporter.

reference

An optional reference AffymetrixCelFile.

Fields and Methods

Methods:

	`addColorMap`	-
	`getColorMaps`	-
	`plotMargins`	-
	`process`	-
	`setColorMaps`	-

Methods inherited from AffymetrixCelSetReporter:
as.character, getChipType, getDataSet, getPath, nbrOfArrays

Methods inherited from AffymetrixFileSetReporter:
getFileSet, getInputName, getInputTags

Author(s)

Henrik Bengtsson

The TransformReport class

Description

Package: aroma.affymetrix
Class TransformReport

Object
~~|
~~+--TransformReport

Directly known subclasses:

public static class TransformReport
extends Object

Usage

TransformReport(inSet=NULL, outSet=NULL, ...)

Arguments

inSet

The input data set as an AffymetrixCelSet.

outSet

The output data set as an AffymetrixCelSet.

...

Not used.

Fields and Methods

Methods:

	`getCdf`	-
	`getFullName`	-
	`getInputDataSet`	-
	`getName`	-
	`getOutputDataSet`	-
	`getPath`	-
	`getTags`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`getYY`	-
	`nbrOfArrays`	-
	`plotXYCurve`	-
	`plotXYCurveLog2`	-
	`seq`	-
	`writeImageCombined`	-
	`writeImages`	-

Author(s)

Henrik Bengtsson

The UgpGenomeInformation class

Description

Package: aroma.affymetrix
Class UgpGenomeInformation

Directly known subclasses:

public abstract static class UgpGenomeInformation
extends GenomeInformation

This class represents Aroma UGP genome information files.

Usage

UgpGenomeInformation(..., .ugp=NULL, .verify=TRUE)

Arguments

...

Arguments passed to GenomeInformation.

.ugp

For internal use only.

.verify

For internal use only.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getChromosomes`	-
	`getData`	-
	`getUnitsOnChromosome`	-
	`isCompatibleWithCdf`	-
	`nbrOfUnits`	-
	`readDataFrame`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

Defines a UgpGenomeInformation object by chip type

Description

Defines a UgpGenomeInformation object by chip type.

Usage

## Static method (use this):
## UgpGenomeInformation$byChipType(chipType, tags=NULL, ..., nbrOfUnits=NULL,
##   verbose=FALSE)

## Don't use the below:
## S3 method for class 'UgpGenomeInformation'
byChipType(static, chipType, tags=NULL, ..., nbrOfUnits=NULL, verbose=FALSE)

Arguments

chipType

A character string.

tags

...

...

Additional arguments passed to UgpGenomeInformation.

verbose

See Verbose.

Value

Returns an UgpGenomeInformation object. If no file was not found, an error is thrown.

The UnitModel class

Description

Package: aroma.affymetrix
Class UnitModel

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--UnitModel

Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AlleleSummation, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, FirmaModel, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, MultiArrayUnitModel, ProbeLevelModel, RmaCnPlm, RmaPlm, RmaSnpPlm, SingleArrayUnitModel

public abstract static class UnitModel
extends Model

This class is abstract and represents a generic unit model, i.e. a model that is applied to each unit separately.

Usage

UnitModel(dataSet=NULL, probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm"),
  shift=0, ...)

Arguments

dataSet

An AffymetrixCelSet to which this model should be fitted.

probeModel

A character string specifying how PM and MM values should be modeled. By default only PM signals are used.

shift

An optional amount the signals should be shifted (translated) before fitting the model.

...

Arguments passed to the constructor of Model.

Fields and Methods

Methods:

	`findUnitsTodo`	-

Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The UnitTypeScaleNormalization class

Description

Package: aroma.affymetrix
Class UnitTypeScaleNormalization

Directly known subclasses:

public static class UnitTypeScaleNormalization
extends ProbeLevelTransform3

This class represents a normalization function that transforms the probe signals such that each unit type gets the same average.

Usage

UnitTypeScaleNormalization(..., targetAvg=4400)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform3.

targetAvg

A numeric value.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The WeightsFile class

Description

Package: aroma.affymetrix
Class WeightsFile

Directly known subclasses:

public abstract static class WeightsFile
extends ParameterCelFile

This class represents weights calculated from residuals of probe-level models.

Usage

WeightsFile(..., probeModel=c("pm"))

Arguments

...

Arguments passed to ParameterCelFile.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getImage`	-
	`readUnits`	-
	`writeImage`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson, Ken Simpson

The WeightsSet class

Description

Package: aroma.affymetrix
Class WeightsSet

Directly known subclasses:

public static class WeightsSet
extends ParametersInterface

This class represents probe-level weights.

Usage

WeightsSet(..., probeModel=c("pm"))

Arguments

...

Arguments passed to AffymetrixCelSet.

probeModel

The specific type of model, e.g. "pm".

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getAverageFile`	-
	`getCellIndices`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson, Ken Simpson

Coerce an object to an AffymetrixCelSet object

Description

Coerce an object to an AffymetrixCelSet object.

Usage

## S3 method for class 'AffymetrixCelSet'
as.AffymetrixCelSet(object, ...)

Arguments

...

Other arguments passed to list.files().

Value

Returns an AffymetrixCelSet object.

Author(s)

Henrik Bengtsson

Coerce an object to an AffymetrixCnChpSet object

Description

Coerce an object to an AffymetrixCnChpSet object.

Usage

## S3 method for class 'AffymetrixCnChpSet'
as.AffymetrixCnChpSet(object, ...)

Arguments

...

Other arguments passed to list.files().

Value

Returns an AffymetrixCnChpSet object.

Coerce an object to an AffymetrixFileSet object

Description

Coerce an object to an AffymetrixFileSet object.

Usage

## S3 method for class 'AffymetrixFileSet'
as.AffymetrixFileSet(object, ...)

Arguments

...

Other arguments passed to list.files().

Value

Returns an AffymetrixFileSet object.

Coerce an object to an CnagCfhSet object

Description

Coerce an object to an CnagCfhSet object.

Usage

## S3 method for class 'CnagCfhSet'
as.CnagCfhSet(object, ...)

Arguments

...

Other arguments passed to list.files().

Value

Returns an CnagCfhSet object.

Coerce an object to an DChipDcpSet object

Description

Coerce an object to an DChipDcpSet object.

Usage

## S3 method for class 'DChipDcpSet'
as.DChipDcpSet(object, ...)

Arguments

...

Other arguments passed to list.files().

Value

Returns an DChipDcpSet object.

Returns a short string describing the Affymetrix CEL set

Description

Returns a short string describing the Affymetrix CEL set.

Usage

## S3 method for class 'AffymetrixCelSet'
as.character(x, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Returns a short string describing the set

Description

Returns a short string describing the set.

Usage

## S3 method for class 'AffymetrixCnChpSet'
as.character(x, ...)

Arguments

...

Not used.

Value

Returns a character string.

Returns a short string describing the CNAG CFH set

Description

Returns a short string describing the CNAG CFH set.

Usage

## S3 method for class 'CnagCfhSet'
as.character(x, ...)

Arguments

...

Not used.

Value

Returns a character string.

Returns a short string describing the DChip CHP set

Description

Returns a short string describing the DChip CHP set.

Usage

## S3 method for class 'DChipDcpSet'
as.character(x, ...)

Arguments

...

Not used.

Value

Returns a character string.

Calculates the average empirical distribution across all samples

Description

Calculates the average empirical distribution across all samples.

Usage

## S3 method for class 'AffymetrixCelSet'
averageQuantile(this, probes=NULL, excludeCells=NULL, ..., verbose=FALSE)

Arguments

probes

An optional numeric vector specifying what subset of probes to be used to calculate the empirical distribution. If NULL, all probes are used.

...

Not used.

verbose

See Verbose.

Details

This methods implements Step A2-A3 in the algorithm for quantile normalization proposed by Bengtsson et al. (2008).

Value

Returns a double vector of length N.

Missing values

If NAs are detected in a sample, these are excluded and the approx() function (approx) is used to "expand" the vector of the remaining values so that the sorted vector (still) have length N.

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.

Creates a CDF from tiling-array BPMAP file

Description

Creates a CDF from tiling-array BPMAP file.

NOTE: This method applies only to Affymetrix tiling arrays! Furthermore, it is likely to be more useful for promoter tiling arrays and less so for whole-genome tiling arrays.

Usage

## Default S3 method:
bpmapCluster2Cdf(pathname, chipType, tags=NULL, rows, cols, maxProbeDistance=3000L,
  minNbrOfProbes=30L, groupName=gsub("_.*", "", chipType), field="fullname",
  stringRemove=sprintf("%s:.*;", groupName), ..., flavor=c("v2", "v1"), path="*",
  verbose=-10)

Arguments

pathname

The pathname to the BPMAP file.

chipType, tags

The chip type and optional tags of the CDF to be written.

rows, cols

Two positive integers specifying the probe dimension of the chip. It is important to get this correct. They can be inferred from the CEL header of a CEL file for this chip, cf. readCelHeader.

maxProbeDistance

A positive integer specifying the maximum genomic distance (in basepairs) allowed between two probes in order to "cluster" those two probes into the same CDF units. Whenever the distance is greater, the two probes end up in two different CDF units.

minNbrOfProbes

A positive integer specifying the minimum number of probes required in a CDF unit. If fewer, those probes are dropped.

groupName

A character string specifying which BPMAP sequences to keep. Sequence with this group name is kept, all others are excluded.

field

A character string.

stringRemove

An (optional) regular expression.

...

Optional arguments passed to readBpmap.

flavor

Specifying which version of BPMAP-to-CDF generator to use. The default is always to use the most recent one, which is also the recommended one. Previous versions are kept only for backward compatibility (and may be dropped at anytime).

path

The directory where the CDF file will be written. If "*" (default), it will be written to annotationData/chipTypes/<chipType>/.

verbose

See Verbose.

Details

This method applies only to Affymetrix tiling arrays. It is likely to be useful for promoter tiling arrays and less so for whole-genome tiling arrays. Flavor "v2" replaced "v1" as aroma.affymetrix v2.5.4 (June 21, 2012). For details, see news(package="aroma.affymetrix").

Value

Returns (invisibly) a the pathname of the created CDF file. The created CDF is written to the current directory.

Author(s)

Henrik Bengtsson adopted from Mark Robinson standalone/online version as of July 11, 2011.

Defines a DChipGenomeInformation object by chip type

Description

Defines a DChipGenomeInformation object by chip type.

Usage

## S3 method for class 'DChipGenomeInformation'
byChipType(static, chipType, version=NULL, ..., verbose=FALSE)

Arguments

chipType

A character string.

version

An optional character string specifying the version string, if more than one version is available.

...

Not used.

verbose

See Verbose.

Value

Returns an DChipGenomeInformation object. If no file was not found, an error is thrown.

Defines a DChipSnpInformation object by chip type

Description

Defines a DChipSnpInformation object by chip type.

Usage

## S3 method for class 'DChipSnpInformation'
byChipType(static, chipType, version=NULL, ...)

Arguments

chipType

A character string.

version

An optional character string specifying the version string, if more than one version is available.

...

Additional arguments passed to *findByChipType().

Value

Returns an DChipSnpInformation object. If no file was not found, an error is thrown.

Static method to define a genome information set by chip type

Description

Static method to define a genome information set by chip type.

Usage

## S3 method for class 'SnpInformation'
byChipType(...)

Arguments

...

Not used.

Value

Returns a SnpInformation object.

Estimates the baseline signal chromosome by chromosome

Description

Estimates the baseline signal chromosome by chromosome.

Usage

## S3 method for class 'ChipEffectSet'
calculateBaseline(this, chromosomes=NULL, ploidy=2, defaultPloidy=NA, all=FALSE,
  force=FALSE, verbose=FALSE, ...)

Arguments

chromosomes

An integer vector specifying for which chromsosomes the baseline should be estimated. If NULL, all chromosomes are considered.

ploidy

An integer specifying the ploidy that the baseline should have.

defaultPloidy

An integer specifying the default ploidy of chromosomes that have not explicitly been allocated one.

all

If TRUE, signals are averaged also for cells that are not on the genome.

force

If TRUE, the CEL file that stores the is recreated.

verbose

See Verbose.

...

Not used.

Author(s)

Henrik Bengtsson

Computes parameters for adjustment of specific binding

Description

Computes parameters for adjustment of specific binding.

Usage

## S3 method for class 'AffymetrixCelSet'
calculateParametersGsb(this, nbrOfPms=25000, affinities=NULL, seed=NULL, ...,
  verbose=FALSE)

Arguments

nbrOfPms

The number of random PMs to use in estimation.

affinities

A numeric vector of probe affinities.

seed

An (optional) integer specifying a temporary random seed to be used during processing. The random seed is set to its original state when done. If NULL, it is not set.

...

Not used.

verbose

See Verbose.

Details

This method is not constant in memory! /HB 2007-03-26

Author(s)

Ken Simpson

Gets the set of residuals corresponding to the PLM

Description

Gets the set of residuals corresponding to the PLM.

Usage

## S3 method for class 'FirmaModel'
calculateResidualSet(this, ...)

Arguments

...

Not used.

Value

Returns a ResidualSet object.

Checks if two AffymetrixCdfFile objects are equal

Description

Checks if two AffymetrixCdfFile objects are equal.

Usage

## S3 method for class 'AffymetrixCdfFile'
compare(this, other, ...)

Arguments

other

The other AffymetrixCdfFile object to be compared to.

...

Additional arguments passed to compareCdfs.

Value

Returns TRUE if the two objects are equal, otherwise FALSE.

Calculates probe affinities from sequence

Description

Calculates probe affinities from sequence.

Adapted from compute.affinities in the gcrma package. Attempts to find the tab-separated probe sequence file associated with a particular CDF, and matches sequence to probe index in order to assign an affinity to each probe.

Usage

## S3 method for class 'AffymetrixCdfFile'
computeAffinities(this, safe=TRUE, force=FALSE, verbose=FALSE, ...)

Arguments

safe

A logical argument passed to getProbeSequenceData().

force

If FALSE, cached results is returned, if available.

verbose

See Verbose.

...

Not used.

Value

Returns a numeric vector of (log2) probe affinities, of length equal to the total number of features on the array.

Author(s)

Ken Simpson, Henrik Bengtsson, Mark Robinson

Converts a CDF into the same CDF but with another format

Description

Converts a CDF into the same CDF but with another format.

Usage

## S3 method for class 'AffymetrixCdfFile'
convert(this, chipType=getChipType(this), suffix=NULL, sep="-", path="cdf", ...,
  verbose=FALSE)

Arguments

chipType

The chip type of the new CDF.

suffix

A suffix added to the chip type of the new CDF.

sep

A string separating the chip type and the suffix string.

path

The path where to store the new CDF file.

...

Additional arguments passed to convertCdf.

verbose

A logical or Verbose.

Value

Returns the new CDF as an AffymetrixCdfFile object.

Gets and validates unit indices

Description

Gets and validates unit indices either by unit names or by a unit indices (validation).

Usage

## S3 method for class 'AffymetrixCdfFile'
convertUnits(this, units=NULL, keepNULL=FALSE, ...)

Arguments

units

Either a character vector with unit names, or an integer vector with unit indices to be validated. If NULL, all unit indices are returned.

keepNULL

If TRUE, NULL returns NULL.

...

Not used.

Value

Returns an integer vector with unit indices. If some units are non existing, an error is thrown.

Creates an exon-by-transcript CDF

Description

Creates an exon-by-transcript CDF based on the probesets defined in an "exon-only" CDF and transcript-exon mapping of a NetAffx probeset annotation data file.

Usage

## S3 method for class 'AffymetrixCdfFile'
createExonByTranscriptCdf(cdf, csv, tags=c("*"), path=getPath(cdf),
  type=c("all", "core", "extended", "full", "main", "control", "cds"), subsetBy=NULL,
  within=NULL, ..., overwrite=FALSE, verbose=FALSE)

Arguments

cdf

An AffymetrixCdfFile specifying an "exon-only" CDF, which defines the exon-specific probesets that will go into the new CDF. For more details, see below.

csv

An AffymetrixNetAffxCsvFile specifying the Affymetrix NetAffx CSV probeset annotation file that contains the transcript-exon mapping.

tags

Additional tags added to the filename of created CDF, i.e. <chiptype>,<tags>.cdf.

path

The output path where the custom CDF will be written.

type

A character string specifying the type of CDF to be written.

subsetBy

An optional character specifying the name of a column in the annotation file to subset against. The column will be parsed as the data type of argument within.

within

A vector of values accepted for the subsetBy column.

...

Additional arguments passed to readDataFrame() of AffymetrixNetAffxCsvFile, e.g. nrow.

overwrite

If TRUE, an existing CDF is overwritten.

verbose

...

Value

Returns an AffymetrixCdfFile.

Requirements for the "exon-only" CDF

The template CDF - argument cdf - should be an "exon-only" CDF: each unit has one group/probeset, which is the exon. An example of this is the "unsupported" HuEx-1_0-st-v2.cdf from Affymetrix, which has 1,432,154 units. Such "exon-only" CDFs do not contain information about clustering exons/probesets into gene transcripts. The CDF may also contain a number of non-exon probesets corresponding to control probes, which can contain very large numbers of probes per probeset. Such units are dropped/ignored by this method.

Ordering of transcripts and exons within transcripts

The transcripts (=units) will be ordered as they appear in the NetAffx annotation file. Within each transcript (=unit), the exons (=groups) are ordered lexicographically by their names.

Naming of transcripts and exons

In the created CDF, each unit corresponds to one transcript cluster, and each group within a unit corresponds to the exons within that transcript cluster. Thus, the unit names correspond to the transcript cluster names and the group names correspond to the exon names.

The exon names are defined by unit names of the exon-only CDF, whereas the transcript names are defined by the transcriptClusterId column in the NetAffx annotation data file. These transcript and exon names are often "non-sense" integers. In order to map these to more genome-friendly names, use the various annotations available in the NetAffx annotation data file.

Author(s)

Henrik Bengtsson adopted from createTranscriptCDF() written by Ken Simpson, Elizabeth Purdom and Mark Robinson.

Examples

## Not run: 
# The exon-only CDF
cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")

# The NetAffx probeset annotation data file
csv <- AffymetrixNetAffxCsvFile("HuEx-1_0-st-v2.na24.hg18.probeset.csv", path=getPath(cdf))

# Create a CDF containing all core probesets:
cdfT <- createExonByTranscriptCdf(cdf, csv=csv, tags=c("*,HB20110911"))
print(cdfT)

# Create CDF containing the core probesets with 3 or 4 probes:
cdfT2 <- createExonByTranscriptCdf(cdf, csv=csv,
            tags=c("*,bySize=3-4,HB20110911"),
            subsetBy="probeCount", within=c("3", "4"))
print(cdfT2)

## End(Not run)

Creates a CEL file using another as a template

Description

Creates a CEL file using another as a template.

Usage

## S3 method for class 'AffymetrixCelFile'
createFrom(this, filename, path=NULL, overwrite=FALSE, skip=!overwrite,
  version=c("4", "3"), methods=c("copy", "create"), clear=FALSE, defValue=0, ...,
  verbose=FALSE)

Arguments

filename, path

The filename and path of to the CEL file to be created.

version

The file-format version of the CEL file to be created.

methods

If "copy", the new file is created as a copy of the template file. If "create", the new file is created from scratch from the template file.

clear

If TRUE, the fields of the CEL file are cleared (zeroed), otherwise they contain the same information as the source file.

defValue

A numeric value that cleared/allocated elements have.

...

Not used.

verbose

See "R.utils::Verbose".

Value

Returns a AffymetrixCelFile reference to the new CEL file.

Author(s)

Henrik Bengtsson

Creates a mono-cell version of the CDF

Description

Creates a mono-cell version of the CDF.

Usage

## S3 method for class 'AffymetrixCdfFile'
createMonocellCdf(this, chipType=getChipType(this), tags="monocell", path=NULL,
  nbrOfCellsPerField=1, ..., ram=NULL, overwrite=FALSE, verbose=TRUE)

Arguments

chipType

The chip type of the new CDF.

tags

Tags added to the chip type of the new CDF.

path

The path where to store the new CDF file.

nbrOfCellsPerField

Number of cells per group field the new CDF should have.

...

Additional arguments passed to writeCdf.

ram

A double saying if more or less units should be converted per chunk. A smaller value uses less memory.

verbose

A logical or Verbose.

Value

Returns the monocell CDF as an AffymetrixCdfFile object.

Author(s)

Henrik Bengtsson, Ken Simpson

Creates a unique-cell version of the CDF

Description

In some cases, single probes map to multiple genome locations. In cases where you may later want to store a probe estimate (e.g. a probe effect or a residual), you will not be able to store more than one per cell. The unique CDF facilitates this by making the cell indices unique (essentially copying the multimapping probes).

Usage

## S3 method for class 'AffymetrixCdfFile'
createUniqueCdf(this, chipType=getChipType(this), tags="unique", path=NULL, units=NULL,
  ..., ram=NULL, verbose=TRUE)

Arguments

chipType

The chip type of the new CDF.

tags

Tags added to the chip type of the new CDF.

path

The path where to store the new CDF file.

...

Additional arguments passed to writeCdf.

ram

A double saying if more or less units should be converted per chunk. A smaller value uses less memory.

verbose

A logical or Verbose.

Details

Note that the set of units in the "unique" CDF is identical to that of the input CDF. So are the unit groups in each unit. Also the number of cells per unit group is preserved. It is only the cell-index composition of each unit group that changes. The cell indices in the unique CDF are guaranteed to occur only once, whereas this may not be true for the input CDF.

Value

Returns the unique CDF as an AffymetrixCdfFile object.

Author(s)

Mark Robinson

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)

Description

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

Usage

  ## S3 method for class 'AffymetrixCelSet'
doCRMAv1(csR, shift=+300, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, drop=TRUE,
  verbose=FALSE, ...)
  ## Default S3 method:
doCRMAv1(dataSet, ..., verbose=FALSE)
  ## Default S3 method:
doASCRMAv1(...)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).

shift

An tuning parameter specifying how much to shift the probe signals before probe summarization.

combineAlleles

A logical specifying whether allele probe pairs should be summed before modeling or not.

lengthRange

An optional numeric vector of length two passed to FragmentLengthNormalization.

arrays

A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.

drop

If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.

verbose

See Verbose.

...

Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Allele-specific or only total-SNP signals

If you wish to obtain allele-specific estimates for SNPs, which are needed to call genotypes or infer parent-specific copy numbers, then use argument combineAlleles=FALSE. Total copy number signals are still available. If you know for certain that you will not use allele-specific estimates, you will get slightly less noisy signals (very small difference) if you use combineAlleles=TRUE.

doASCRMAv1(...) is a wrapper for doCRMAv1(..., combineAlleles=FALSE).

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)

Description

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

We recommend CRMA v2 for estimating allele-specific as well total SNP signals from Affymetrix SNP chips.

Usage

  ## S3 method for class 'AffymetrixCelSet'
doCRMAv2(csR, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL,
  plm=c("AvgCnPlm", "RmaCnPlm"), drop=TRUE, verbose=FALSE, ...)
  ## Default S3 method:
doCRMAv2(dataSet, ..., verbose=FALSE)
  ## Default S3 method:
doASCRMAv2(...)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).

combineAlleles

A logical specifying whether allele probe pairs should be summed before modeling or not.

lengthRange

An optional numeric vector of length two passed to FragmentLengthNormalization.

arrays

A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.

plm

A character string specifying which type of probe-summarization model to used.

drop

If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.

verbose

See Verbose.

...

Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Allele-specific or only total-SNP signals

doASCRMAv2(...) is a wrapper for doCRMAv2(..., combineAlleles=FALSE).

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, P. Wirapati & T.P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, Bioinformatics, 2009.

Finding Isoforms using Robust Multichip Analysis (FIRMA)

Description

Finding Isoforms using Robust Multichip Analysis (FIRMA) based on [1].

Usage

  ## S3 method for class 'AffymetrixCelSet'
doFIRMA(csR, ..., flavor=c("v1b", "v1a"), drop=TRUE, verbose=FALSE)
  ## Default S3 method:
doFIRMA(dataSet, ..., verbose=FALSE)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).

...

Additional arguments passed to FirmaModel, and to set up AffymetrixCelSet (when argument dataSet is specified).

flavor

A character string specifying the flavor of FIRMA to use.

drop

If TRUE, the FIRMA scores are returned, otherwise a named list of all intermediate and final results.

verbose

See Verbose.

Value

Returns a named list, iff drop == FALSE, otherwise only FirmaSet object (containing the FIRMA scores).

Using a custom exon-by-transcript CDF

It is strongly recommended to use a custom CDF, e.g. "core", "extended" or "full" [1]. To use a custom CDF, set it before calling this method, i.e. setCdf(csR, cdf). Do not set the standard "non-supported" Affymetrix CDF (see also Section 'Flavors').

Flavors

If flavor == "v1b" (default), then the standard "non-supported" Affymetrix CDF is used for background correction and the quantile normalization steps, and the custom CDF is used for the probe summarization and everything that follows. The advantage of this flavor is that those two first preprocessing steps will remain the same if one later changes to a different custom CDF.

If flavor == "v1a", then the custom CDF is used throughout all steps of FIRMA, which means that if one changes the custom CDF all steps will be redone.

Author(s)

Henrik Bengtsson

References

[1] E. Purdom, K. Simpson, M. Robinson, J. Conboy, A. Lapuk & T.P. Speed, FIRMA: a method for detection of alternative splicing from exon array data, Bioinformatics, 2008.

Robust Multichip Analysis (GCRMA)

Description

Robust Multichip Analysis (GCRMA) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems. The method replicates the results of gcrma (package gcrma) with great precision.

Usage

  ## S3 method for class 'AffymetrixCelSet'
doGCRMA(csR, arrays=NULL, type=c("fullmodel", "affinities"), uniquePlm=FALSE, drop=TRUE,
  verbose=FALSE, ...)
  ## Default S3 method:
doGCRMA(dataSet, ..., verbose=FALSE)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).

arrays

A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.

type

A character string specifying what type of model to use for the GCRMA background correction. For more details, see GcRmaBackgroundCorrection.

uniquePlm

If TRUE, the log-additive probe-summarization model is done on probeset with unique sets of probes. If FALSE, the summarization is done on "as-is" probesets as specified by the CDF.

drop

If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.

verbose

See Verbose.

...

Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Author(s)

Henrik Bengtsson

References

[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer. A Model Based Background Adjustment for Oligonucleotide Expression Arrays, JASA, 2004.

Robust Multichip Analysis (RMA)

Description

Robust Multichip Analysis (RMA) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems. The method replicates the results of fitPLM (package affyPLM) with great precision.

Usage

  ## S3 method for class 'AffymetrixCelSet'
doRMA(csR, arrays=NULL, flavor=c("affyPLM", "oligo"), uniquePlm=FALSE, drop=TRUE,
  verbose=FALSE, ...)
  ## Default S3 method:
doRMA(dataSet, ..., verbose=FALSE)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).

arrays

A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.

flavor

A character string specifying what model fitting algorithm to be used, cf. RmaPlm.

uniquePlm

If TRUE, the log-additive probe-summarization model is done on probeset with unique sets of probes. If FALSE, the summarization is done on "as-is" probesets as specified by the CDF.

drop

If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.

verbose

See Verbose.

...

Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Author(s)

Henrik Bengtsson

References

[1] Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

Extracts an in-memory AffyBatch object from the CEL set

Description

Extracts an in-memory AffyBatch object from the CEL set. Note that any modifications done to the extract object will not be reflected in the original CEL set.

Usage

## S3 method for class 'AffymetrixCelSet'
extractAffyBatch(this, ..., verbose=FALSE)

Arguments

...

Argument passed to ReadAffy() (read.affybatch).

verbose

See Verbose.

Details

Since the affy package is making use of special CDF environment packages, this method will warn if the needed package is missing and explain that affy will later try to download and install it automatically.

Value

Returns an AffyBatch-class object.

Author(s)

Henrik Bengtsson

Extract data as a data.frame for a set of arrays

Description

Extract data as a data.frame for a set of arrays.

Usage

## S3 method for class 'ParameterCelSet'
extractDataFrame(this, addNames=FALSE, addUgcMap=TRUE, ..., drop=FALSE, verbose=FALSE)

Arguments

...

Arguments passed to *extractMatrix().

addNames

If TRUE, the first two columns contain the unit names and the group names according the the CDF, otherwise those two columns are not included.

addUgcMap

If TRUE, the columns following the unit and group names contains the (unit, group, cell) index map.

verbose

See Verbose.

Value

Returns a Jx(2+3+K) data.frame where J is the number of units, and K is the number of arrays. The first two columns, if addNames=TRUE, contains the unit names and the group names. The next three columns contains the (unit, group, cell) index map. The last K columns named by the arrays contain the data for the K arrays. No names are set for the rows. The rows are ordered according to units arguments.

Author(s)

Henrik Bengtsson

Extracts an in-memory ExpressionSet object

Description

Extracts an in-memory ExpressionSet object from a ChipEffectSet object. Note that any modifications done to the extracted object will not be reflected in the original chip-effect set.

Usage

## S3 method for class 'ChipEffectSet'
extractExpressionSet(this, ..., logBase=2, orderUnitsBy=c("asis", "lexicographic"),
  annotationPkg=NULL, verbose=FALSE)

Arguments

...

Optional argument passed to *extractMatrix().

logBase

An integer specifying the base to use when log-transforming the signals. If NULL, the signals are not transformed, but kept as is.

annotationPkg

(optional) A character string specifies a Bioconductor (ChipDb, CDF environment or PDInfo) annotation package, which then sets the 'annotation' slot of the returned object. If "ChipDb", "cdf" or "PDInfo" th corresponding ChipDB, CDF environment or PDInfo package is inferred from the CDF's chip type.

verbose

See Verbose.

Value

Returns an ExpressionSet-class object.

Author(s)

Henrik Bengtsson

Extracts CEL signals an in-memory FeatureSet object

Description

Extracts CEL signals an in-memory FeatureSet object from a AffymetrixCelSet object. Note that any modifications done to the extracted object will not be reflected in the original CEL set.

Usage

## S3 method for class 'AffymetrixCelSet'
extractFeatureSet(this, ..., verbose=FALSE)

Arguments

...

Additional argument passed to read.celfiles.

verbose

See Verbose.

Value

Returns an FeatureSet-class object.

Author(s)

Henrik Bengtsson

Extract data as a matrix for a set of arrays

Description

Extract data as a matrix for a set of arrays.

Usage

## S3 method for class 'AffymetrixCelSet'
extractMatrix(this, cells=NULL, ..., field=c("intensities", "stdvs", "pixels"),
  drop=FALSE, verbose=FALSE)

Arguments

cells

(The subset of cells to be matched. If NULL, all cells are considered.

...

Not used.

field

The field to be extracted.

drop

If TRUE, singleton dimensions are dropped.

verbose

See Verbose.

Value

Returns an JxK double matrix where J is the number of units, and K is the number of arrays. The names of the columns are the names of the arrays. No names are set for the rows. The rows are ordered according to cells argument.

Author(s)

Henrik Bengtsson, Mark Robinson

Extract data as a matrix for a set of arrays

Description

Extract data as a matrix for a set of arrays.

Usage

## S3 method for class 'ParameterCelSet'
extractMatrix(this, units=NULL, ..., field=c("intensities", "stdvs", "pixels"),
  returnUgcMap=FALSE, drop=FALSE, verbose=FALSE)

Arguments

units

(The subset of units to be matched. If NULL, all units are considered.

...

Passed to subset() operating on the UGC map.

field

The field to be extracted.

returnUgcMap

If TRUE, the (unit, group, cell) map is returned as an attribute.

drop

If TRUE, singleton dimensions are dropped.

verbose

See Verbose.

Value

Author(s)

Henrik Bengtsson

Locates an annotation file by its chip type

Description

Locates an annotation file by its chip type.

Usage

## S3 method for class 'AromaChipTypeAnnotationFile'
findByChipType(...)

Arguments

...

Additional arguments.

Value

Returns the pathname (as a character string) to the first annotation chip type file found. If no one was found, NULL is returned.

Identifies non-fitted units

Description

Identifies non-fitted units.

Usage

## S3 method for class 'FirmaModel'
findUnitsTodo(this, ...)

Arguments

...

Not used.

Value

Returns an integer vector of unit indices.

Identifies non-fitted units

Description

Identifies non-fitted units.

Usage

## S3 method for class 'ProbeLevelModel'
findUnitsTodo(this, verbose=FALSE, ...)

Arguments

verbose

A logical or a Verbose.

...

Not used.

Value

Returns an integer vector of unit indices.

Identifies non-fitted units

Description

Identifies non-fitted units.

Usage

## S3 method for class 'UnitModel'
findUnitsTodo(...)

Arguments

...

Arguments specific to any subclass.

Value

Returns an integer vector of unit indices.

Estimates the model parameters

Description

Estimates the model parameters for all or a subset of the units.

Usage

## S3 method for class 'FirmaModel'
fit(this, units="remaining", ..., ram=NULL, force=FALSE, verbose=FALSE)

Arguments

units

The units to be fitted. If NULL, all units are considered. If remaining, only non-fitted units are considered.

...

Arguments passed to readUnits().

ram

A double indicating if more or less units should be loaded into memory at the same time.

force

If TRUE, already fitted units are re-fitted, and cached data is re-read.

verbose

See Verbose.

Details

All estimates are stored to file.

The non-array specific parameter estimates together with standard deviation estimates and convergence information are stored in one file.

The parameter estimates specific to each array, typically "chip effects", are stored in array specific files.

Data set specific estimates [L = number of probes]: phi [L doubles] (probe affinities), sd(phi) [L doubles], isOutlier(phi) [L logicals]

Algorithm-specific results: iter [1 integer], convergence1 [1 logical], convergence2 [1 logical] dTheta [1 double] sd(eps) - [1 double] estimated standard deviation of the error term

Array-specific estimates [K = nbr of arrays]: theta [K doubles] (chip effects), sd(theta) [K doubles], isOutlier(theta) [K logicals]

For each array and each unit group, we store: 1 theta, 1 sd(theta), 1 isOutlier(theta), i.e. (float, float, bit) => For each array and each unit (with G_j groups), we store: G_j theta, G_j sd(theta), G_j isOutlier(theta), i.e. G_j*(float, float, bit). For optimal access we store all thetas first, then all sd(theta) and the all isOutlier(theta). To keep track of the number of groups in each unit, we have to have a (unit, ngroups) map. This can be obtained from getUnitNames() for the AffymetrixCdfFile class.

Value

Returns an integer vector of indices of the units fitted, or NULL if no units was (had to be) fitted.

Estimates the model parameters

Description

Estimates the model parameters.

Usage

## S3 method for class 'Model'
fit(...)

Arguments

...

Arguments specific to any subclass.

Value

Returns an integer vector specifying what units where fitted.

Estimates the model parameters

Description

Estimates the model parameters for all or a subset of the units.

Usage

## S3 method for class 'ProbeLevelModel'
fit(this, units="remaining", ..., force=FALSE, ram=NULL, verbose=FALSE)

Arguments

units

The units to be fitted. If NULL, all units are considered. If remaining, only non-fitted units are considered.

...

Arguments passed to readUnits().

force

If TRUE, already fitted units are re-fitted, and cached data is re-read.

ram

A double indicating if more or less units should be loaded into memory at the same time.

verbose

See Verbose.

Details

All estimates are stored to file.

The non-array specific parameter estimates together with standard deviation estimates and convergence information are stored in one file.

The parameter estimates specific to each array, typically "chip effects", are stored in array specific files.

Data set specific estimates [L = number of probes]: phi [L doubles] (probe affinities), sd(phi) [L doubles], isOutlier(phi) [L logicals]

Algorithm-specific results: iter [1 integer], convergence1 [1 logical], convergence2 [1 logical] dTheta [1 double] sd(eps) - [1 double] estimated standard deviation of the error term

Array-specific estimates [K = nbr of arrays]: theta [K doubles] (chip effects), sd(theta) [K doubles], isOutlier(theta) [K logicals]

Value

Returns an integer vector of indices of the units fitted, or NULL if no units was (had to be) fitted.

Author(s)

Henrik Bengtsson

Estimates the model parameters

Description

Estimates the model parameters for all or a subset of the units.

Usage

## S3 method for class 'SingleArrayUnitModel'
fit(this, arrays=NULL, units="remaining", ..., force=FALSE, verbose=FALSE)

Arguments

arrays

The arrays to be fitted. If NULL, all arrays are considered. If remaining, only non-fitted arrays are considered.

units

The units to be fitted. If NULL, all units are considered. If remaining, only non-fitted units are considered.

...

Arguments passed to *readUnits().

force

If TRUE, already fitted units are re-fitted, and cached data is re-read.

verbose

See Verbose.

Details

All estimates are stored to file.

The parameter estimates specific to each array, typically "chip effects", are stored in array specific files.

Array-specific estimates [K = nbr of arrays]: theta [K doubles] (chip effects), sd(theta) [K doubles], isOutlier(theta) [K logicals]

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Fits the model for one chromosome across samples

Description

Fits the model for one chromosome across samples.

Usage

## S3 method for class 'SmoothMultiarrayModel'
fit(this, chromosome, force=FALSE, ..., verbose=FALSE)

Arguments

chromosome

An integer specifying the index of the chromosome to be fitted.

...

Additional arguments passed down to the internal fit function.

verbose

See Verbose.

Author(s)

Henrik Bengtsson

Fits quantile normalization functions for the arrays in the data set

Description

Fits quantile normalization functions for the arrays in the data set.

Usage

## S3 method for class 'AffymetrixCelFile'
fitQuantileNormFcn(this, yTarget, subset=NULL, ..., spar=NULL, nknots=1024,
  verbose=FALSE)

Arguments

yTarget

The target probe signals.

subset

An optional numeric vector specifying the indices of the subset of probes to be used to fit the normalization function.

spar, nknots

Control parameters passed to smooth.spline.

...

Not used.

verbose

See Verbose.

Value

Returns a normalization function.

Author(s)

Henrik Bengtsson

Gets the log-intensities and log-ratios of chip effects for two arrays

Description

Gets the log-intensities and log-ratios of chip effects for two arrays.

Usage

## S3 method for class 'ChipEffectFile'
getAM(this, other, units=NULL, ..., verbose=FALSE)

Arguments

other

The second ChipEffectFile object used as the reference.

units

(The subset of units to be matched. If NULL, all units are considered.

...

Not used.

verbose

See Verbose.

Value

Returns a Nx2 matrix where N is the number of units returned. The names of the columns are A (log-intensities) and M (log-ratios). The names of the rows are the unit indices (as indexed by the CDF). The rows are ordered according to units arguments.

Author(s)

Henrik Bengtsson

Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file

Description

Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file.

Usage

## S3 method for class 'ChipEffectSet'
getAM(this, other, units=NULL, ..., verbose=FALSE)

Arguments

other

The second ChipEffectFile object used as the reference.

units

(The subset of units to be matched. If NULL, all units are considered.

...

Not used.

verbose

See Verbose.

Value

Returns an Jx2xK array where J is the number of units, and K is the number of arrays (arrays are always the last dimension). The names of the columns are A (log-intensities) and M (log-ratios). The names of the rows are the unit indices (as indexed by the CDF). The rows are ordered according to units arguments.

Author(s)

Henrik Bengtsson

Gets the alias of the report

Description

Gets the alias of the report.

Usage

## S3 method for class 'GenericReporter'
getAlias(this, ...)

Arguments

...

Not used.

Value

Returns a character, or NULL if no alias is set.

Gets the name alias for the model

Description

Gets the name alias for the model, if set.

Usage

## S3 method for class 'Model'
getAlias(this, ...)

Arguments

...

Not used.

Value

Returns a character string, or NULL.

Gets the cell indices of allele pairs

Description

Gets the cell indices of allele pairs in units of type "genotyping" with 2 or 4 unit groups.

Usage

## S3 method for class 'AffymetrixCdfFile'
getAlleleCellPairs(this, units=NULL, stratifyBy=c("pm", "pmmm", "mm"), force=FALSE, ...,
  verbose=FALSE)

Arguments

units

A integer vector of units to query. If NULL, all units are considered.

stratifyBy

A character string specifying what type of probes to return.

...

Not used.

verbose

A logical or a Verbose object.

Value

Returns a Nx2 integer matrix of cell indices, where each row is a (PMA, PMB) probe pair.

Author(s)

Henrik Bengtsson

Gets the indices of probepairs with the same pair of SNP nucleotides

Description

Gets the indices of probepairs with the same pair of SNP nucleotides. Note that the order of allele A and allele B is irrelevant. For instance, all probepairs with nucleotides (A,T) are calibrated together with all probepairs with nucleotides (T,A) reversed.

Usage

## S3 method for class 'AffymetrixCdfFile'
getAlleleProbePairs(this, units=NULL, ignoreOrder=TRUE, force=FALSE, verbose=FALSE, ...)

Arguments

verbose

A logical or a Verbose object.

...

Not used.

Value

Returns a named list where each element is a two-column matrix where the column names are the nucleotides for the two alleles.

Benchmarking

On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:

Mapping10K_Xba142: 10208 units & 432964 cells: 11 seconds.
Mapping50K_Xba240: 58960 SNPs & 589,600 (PMA,PMB) probe pairs: 11 seconds.

Author(s)

Henrik Bengtsson

Gets the indices of probepairs with the same pair of SNP nucleotides

Description

Usage

## S3 method for class 'AffymetrixCdfFile'
getAlleleProbePairs3(this, units=NULL, ignoreOrder=TRUE, force=FALSE, ..., verbose=FALSE)

Arguments

verbose

A logical or a Verbose object.

...

Not used.

Value

Returns a named list where each element is a two-column matrix where the column names are the nucleotides for the two alleles.

Benchmarking

On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:

Mapping10K_Xba142: 10208 units & 432964 cells: 11 seconds.
Mapping50K_Xba240: 58960 SNPs & 589,600 (PMA,PMB) probe pairs: 11 seconds.

Author(s)

Henrik Bengtsson

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set

Description

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set.

Usage

## S3 method for class 'AffymetrixCelSet'
getAverageFile(this, name=NULL, prefix="average", indices="remaining",
  field=c("intensities", "stdvs"), mean=c("median", "mean"), sd=c("mad", "sd"),
  na.rm=TRUE, g=NULL, h=NULL, ..., cellsPerChunk=moreCells * 10^7/length(this),
  moreCells=1, force=FALSE, verbose=FALSE)

Arguments

name

The label of the calculated parameters. If NULL, a default name format <prefix>-<mean>-<sd> is used.

indices

An integer vector specifying which cells to consider. If "remaining", only parameters for cells that have not been are calculated. If NULL, all cells are used.

mean

A character of a function specifying the function used to calculate the average.

sd

A character of a function specifying the function used to calculate the standard deviation.

na.rm

If TRUE, NAs are excluded before, otherwise not.

...

Not used.

cellsPerChunk

A integer specifying the total number of cells (across arrays) read into memory per chunk.

moreCells

A double scalar indicating if more or less cells should be used per chunk.

force

If TRUE, parameters for cells already calculated are recalculated, otherwise not.

verbose

If TRUE, progress details are printed, otherwise not. May also be a Verbose object.

Details

The parameter estimates are stored as a CEL file of the same class as the data files in the set. The CEL file is named <name>.cel and placed in the directory of the set. Currently there is no specific data class for this file, but the average cell signals are stored as "intensities", the standard deviation of the cell signals as "stddevs", and the number of data points used for each estimate is stored as "pixels".

Value

Returns an AffymetrixCelSet of the same class as the CEL set averaged.

Author(s)

Henrik Bengtsson, Ken Simpson

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CFH set

Description

Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CFH set.

Usage

## S3 method for class 'CnagCfhSet'
getAverageFile(this, name=NULL, prefix="average", indices="remaining",
  field=c("intensities", "stdvs"), mean=c("median", "mean"), sd=c("mad", "sd"),
  na.rm=TRUE, g=NULL, h=NULL, ..., cellsPerChunk=moreCells * 10^7/length(this),
  moreCells=1, force=FALSE, verbose=FALSE)

Arguments

name

The label of the calculated parameters. If NULL, a default name format <prefix>-<mean>-<sd> is used.

indices

An integer vector specifying which cells to consider. If "remaining", only parameters for cells that have not been are calculated. If NULL, all cells are used.

mean

A character of a function specifying the function used to calculate the average.

sd

A character of a function specifying the function used to calculate the standard deviation.

na.rm

If TRUE, NAs are excluded before, otherwise not.

...

Not used.

cellsPerChunk

A integer specifying the total number of cells (across arrays) read into memory per chunk.

moreCells

A double scalar indicating if more or less cells should be used per chunk.

force

If TRUE, parameters for cells already calculated are recalculated, otherwise not.

verbose

If TRUE, progress details are printed, otherwise not. May also be a Verbose object.

Details

The parameter estimates are stored as a CFH file of the same class as the data files in the set. The CFH file is named <name>.cel and placed in the directory of the set. Currently there is no specific data class for this file, but the average cell signals are stored as "intensities", the standard deviation of the cell signals as "stddevs", and the number of data points used for each estimate is stored as "pixels".

Value

Returns an CnagCfhSet of the same class as the CFH set averaged.

Gets the baseline signals across chromosomes

Description

Gets the baseline signals across chromosomes.

Usage

## S3 method for class 'ChipEffectSet'
getBaseline(this, force=FALSE, verbose=FALSE, ...)

Arguments

force

If TRUE, the CEL file that stores the is recreated.

verbose

See Verbose.

...

Not used.

Author(s)

Henrik Bengtsson

Gets the CDF structure for this CEL file

Description

Gets the CDF structure for this CEL file.

Usage

## S3 method for class 'AffymetrixCelFile'
getCdf(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCdfFile object.

Author(s)

Henrik Bengtsson

Gets the CDF structure for this CEL set

Description

Gets the CDF structure for this CEL set.

Usage

## S3 method for class 'AffymetrixCelSet'
getCdf(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCdfFile object.

Author(s)

Henrik Bengtsson

Gets the CDF structure for this CEL file

Description

Gets the CDF structure for this CEL file.

Usage

## S3 method for class 'CnagCfhFile'
getCdf(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCdfFile object.

Gets the CDF structure for this CFH set

Description

Gets the CDF structure for this CFH set.

Usage

## S3 method for class 'CnagCfhSet'
getCdf(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCdfFile object.

Gets the CDF structure for this model

Description

Gets the CDF structure for this model.

Usage

## S3 method for class 'Model'
getCdf(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCdfFile object.

Gets the cell indices unit by unit

Description

Gets the cell indices unit by unit of all or a subset of the units.

Usage

## S3 method for class 'AffymetrixCdfFile'
getCellIndices(this, units=NULL, ..., useNames=TRUE, unlist=FALSE, force=FALSE,
  cache=TRUE, verbose=FALSE)

Arguments

units

The units of interest. If NULL, all units are considered.

...

Additional arguments passed to readCdfCellIndices.

useNames

If TRUE, element names are returned, otherwise not.

unlist

If TRUE, the unlisted result is returned. Using this argument is more memory efficient that calling unlist() afterwards.

force

If TRUE, cached values are ignored.

cache

If TRUE, results are cached, if not too large.

verbose

A logical or Verbose.

Details

Note, that it is much more memory efficient to do getCellIndices(cdf, useNames=FALSE, unlist=TRUE) compare with unlist(getCellIndices(cdf), use.names=FALSE).

Value

Returns the list structure returned by readCdfCellIndices.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'ChipEffectFile'
getCellIndices(this, ..., .cache=TRUE)

Arguments

...

Additional arguments passed to getCellIndices() of AffymetrixCdfFile.

.cache

Ignored.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units.

Usage

## S3 method for class 'CnChipEffectFile'
getCellIndices(this, units=NULL, ..., unlist=FALSE, force=FALSE, .cache=TRUE,
  verbose=FALSE)

Arguments

units

Unit indices to be retrieved. If NULL, all units are considered.

...

Additional arguments passed to getCellIndices() of ChipEffectFile.

unlist

If TRUE, the cell indices are returned as a vector.

force

If TRUE, the cell indices are re-read regardless whether they are already cached in memory or not.

.cache

(internal) If TRUE, the result is cached in memory.

verbose

See Verbose.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'CnProbeAffinityFile'
getCellIndices(this, ..., unlist=FALSE)

Arguments

...

Additional arguments passed to getCellIndices() of SnpProbeAffinityFile.

unlist

If TRUE, the cell indices are returned as a vector.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units.

Usage

## S3 method for class 'ExonChipEffectFile'
getCellIndices(this, ..., unlist=FALSE, force=FALSE, .cache=TRUE, verbose=FALSE)

Arguments

...

Additional arguments passed to getCellIndices() of ChipEffectFile.

unlist

If TRUE, the cell indices are returned as a vector.

force

If TRUE, the cell indices are re-read regardless whether they are already cached in memory or not.

.cache

(internal) If TRUE, the result is cached in memory.

verbose

See Verbose.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Author(s)

Henrik Bengtsson

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'ExonProbeAffinityFile'
getCellIndices(this, ..., unlist=FALSE)

Arguments

...

Additional arguments passed to getCellIndices() of ProbeAffinityFile.

unlist

If TRUE, the cell indices are returned as a vector.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'FirmaFile'
getCellIndices(this, ..., .cache=TRUE)

Arguments

...

Additional arguments passed to getCellIndices() of AffymetrixCdfFile.

.cache

Ignored.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'ProbeAffinityFile'
getCellIndices(this, ..., verbose=FALSE)

Arguments

...

Additional arguments passed to getCellIndices() of AffymetrixCdfFile.

verbose

See Verbose.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'ResidualFile'
getCellIndices(this, ..., .cache=TRUE)

Arguments

...

Additional arguments passed to getCellIndices() of AffymetrixCdfFile.

.cache

Ignored.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units.

Usage

## S3 method for class 'SnpChipEffectFile'
getCellIndices(this, units=NULL, ..., unlist=FALSE, force=FALSE, .cache=TRUE,
  verbose=FALSE)

Arguments

units

Unit indices to be retrieved. If NULL, all units are considered.

...

Additional arguments passed to getCellIndices() of ChipEffectFile.

unlist

If TRUE, the cell indices are returned as a vector.

force

If TRUE, the cell indices are re-read regardless whether they are already cached in memory or not.

.cache

(internal) If TRUE, the result is cached in memory.

verbose

See Verbose.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'SnpProbeAffinityFile'
getCellIndices(this, ..., unlist=FALSE)

Arguments

...

Additional arguments passed to getCellIndices() of ProbeAffinityFile.

unlist

If TRUE, the cell indices are returned as a vector.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Gets the cell indices unit by unit

Description

Gets the cell indices unit by unit for all or a subset of units (probesets).

Usage

## S3 method for class 'UnitModel'
getCellIndices(this, ..., verbose=FALSE)

Arguments

...

Additional arguments passed to getCellIndices() of the AffymetrixCdfFile of the input data set.

verbose

See Verbose.

Value

Returns the list structure consisting of CDF cell indices.

Retrieves tree list of cell indices for a set of units

Description

Retrieves tree list of cell indices for a set of units from the associated CDF.

Usage

## S3 method for class 'WeightsFile'
getCellIndices(this, ..., .cache=TRUE)

Arguments

...

Additional arguments passed to getCellIndices() of AffymetrixCdfFile.

.cache

Ignored.

Value

Returns a list structure, where each element corresponds to a unit. If argument unlist=TRUE is passed, an integer vector is returned.

Gets the set of chip effects for this model

Description

Gets the set of chip effects for this model. There is one chip-effect file per array.

Usage

## S3 method for class 'AlleleSummation'
getChipEffectSet(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or a Verbose.

Value

Returns a ChipEffectSet object.

Gets the set of chip effects for this model

Description

Gets the set of chip effects for this model. There is one chip-effect file per array.

Usage

## S3 method for class 'ProbeLevelModel'
getChipEffectSet(this, ..., verbose=FALSE)

Arguments

...

Arguments passed to getMonocellCdf() of AffymetrixCdfFile.

verbose

A logical or a Verbose.

Value

Returns a ChipEffectSet object.

Gets the chip type for this CEL file

Description

Gets the chip type for this CEL file according to the AffymetrixCdfFile object.

Usage

## S3 method for class 'AffymetrixCelFile'
getChipType(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Author(s)

Henrik Bengtsson

Gets the chip type for this CEL set

Description

Gets the chip type for this CEL set. The chip type is inferred from the current CDF.

Usage

## S3 method for class 'AffymetrixCelSet'
getChipType(this, ...)

Arguments

...

Not used.

Value

Returns an character string.

Author(s)

Henrik Bengtsson

Gets the chip type for this CEL file

Description

Gets the chip type for this CEL file according to the AffymetrixCdfFile object.

Usage

## S3 method for class 'CnagCfhFile'
getChipType(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the chip type of this genome information set

Description

Gets the chip type of this genome information set.

Usage

## S3 method for class 'GenomeInformation'
getChipType(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the chip type of this genome information set

Description

Gets the chip type of this genome information set.

Usage

## S3 method for class 'SnpInformation'
getChipType(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the names of the CN units

Description

Gets the names of the CN units.

Usage

## S3 method for class 'AffymetrixCdfFile'
getCnNames(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets all or a subset of the genome information data

Description

Gets all or a subset of the genome information data.

Usage

## S3 method for class 'GenomeInformation'
getData(this, units=NULL, fields=c("chromosome", "physicalPosition"), orderBy=NULL, ...,
  force=FALSE, verbose=FALSE)

Arguments

units

The units for which the data should be returned.

fields

The fields to be returned.

orderBy

The fields by which the returned data frame should be ordered.

...

Named arguments used to select a subset of the units to be returned. Either a value to be compared to or a function returning TRUE or FALSE.

Value

Returns a data.frame, where the row names correspond to unit indices as defined by the annotation unit names file.

Gets all or a subset of the genome information data

Description

Gets all or a subset of the genome information data.

Usage

## S3 method for class 'SnpInformation'
getData(this, units=NULL, fields=c("fragmentLength", "start", "stop"), orderBy=NULL, ...,
  force=FALSE, verbose=FALSE)

Arguments

units

The units for which the data should be returned.

fields

The fields to be returned.

orderBy

The fields by which the returned data frame should be ordered.

...

Named arguments used to select a subset of the units to be returned. Either a value to be compared to or a function returning TRUE or FALSE.

Value

Returns a data.frame, where the row names correspond to unit indices as defined by the CDF.

Gets the data set

Description

Gets the data set for which the reporter is generating output.

Usage

## S3 method for class 'AffymetrixCelSetReporter'
getDataSet(this, ...)

Arguments

...

Not used.

Value

Returns a AffymetrixCelSet.

Gets the data set

Description

Gets the data set for which the explorer is displaying it results.

Usage

## S3 method for class 'ArrayExplorer'
getDataSet(this, ...)

Arguments

...

Not used.

Value

Returns a AffymetrixCelSet.

Gets the input data set for this model

Description

Gets the input data set for this model.

Usage

## S3 method for class 'Model'
getDataSet(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCelSet.

Gets the set of FIRMA results for this model

Description

Gets the set of FIRMA results for this model. There is one chip-effect file per array.

Usage

## S3 method for class 'FirmaModel'
getFirmaSet(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or a Verbose.

Value

Returns a FirmaSet object.

Gets the low-level function that fits the PLM

Description

Gets the low-level function that fits the PLM.

Usage

## S3 method for class 'AffinePlm'
getFitUnitGroupFunction(this, ...)

Arguments

...

Not used.

Value

Returns a function.

Author(s)

Henrik Bengtsson

Gets the low-level function that fits the PLM

Description

Gets the low-level function that fits the PLM.

Usage

## S3 method for class 'AvgPlm'
getFitUnitGroupFunction(this, ...)

Arguments

...

Not used.

Value

Returns a function.

Gets the low-level function that fits the Exon PLM

Description

Gets the low-level function that fits the Exon PLM.

Usage

## S3 method for class 'ExonRmaPlm'
getFitUnitGroupFunction(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or Verbose.

Value

Returns a function.

Author(s)

Henrik Bengtsson and Ken Simpson (WEHI) utilizing Ben Bolstad's preprocessCore package.

Static method to get the low-level function that fits the PLM

Description

Static method to get the low-level function that fits the PLM.

Usage

## S3 method for class 'FirmaModel'
getFitUnitGroupFunction(this, ...)

Arguments

...

Not used.

Value

Returns a function.

Gets the low-level function that fits the PLM

Description

Gets the low-level function that fits the PLM.

Usage

## S3 method for class 'HetLogAddPlm'
getFitUnitGroupFunction(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or Verbose.

Value

Returns a function.

Author(s)

Henrik Bengtsson and Ken Simpson (WEHI) utilizing Ben Bolstad's preprocessCore package.

Gets the low-level function that fits the PLM

Description

Gets the low-level function that fits the PLM.

Usage

## S3 method for class 'MbeiPlm'
getFitUnitGroupFunction(this, ...)

Arguments

...

Not used.

Value

Returns a function.

Gets the low-level function that fits the PLM

Description

Gets the low-level function that fits the PLM.

Usage

## S3 method for class 'RmaPlm'
getFitUnitGroupFunction(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or Verbose.

Value

Returns a function.

Author(s)

Henrik Bengtsson and Ken Simpson (WEHI) utilizing Ben Bolstad's preprocessCore package.

Gets the full name of the output set

Description

Gets the full name of the output set, which consists of the name with appended comma-separated tags.

Usage

## S3 method for class 'Model'
getFullName(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the full name of the output data set

Description

Gets the full name of the output data set, which is the name with comma separated tags.

Usage

## S3 method for class 'TransformReport'
getFullName(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets genome information for this chip type

Description

Gets genome information for this chip type.

Usage

## S3 method for class 'AffymetrixCdfFile'
getGenomeInformation(this, types=c("UGP", "dChip"), ..., force=FALSE, verbose=FALSE)

Arguments

types

A character vector specifying what type of genome information sets to search for.

...

Not used.

force

If FALSE, cached information is retrieved, otherwise not.

verbose

A logical or Verbose.

Value

Returns a GenomeInformation object.

Examples

## Not run: 
 
for (zzz in 0) {

# Define a CDF for a SNP chip
if (!exists("cdf")) {
  cdf <- AffymetrixCdfFile$fromChipType(".*Sty.*")
}
print(cdf)

# Get the genome information
gi <- getGenomeInformation(cdf)
print(gi)

# Get the units on chromosome X order position by default
# (First call will be slow be data is being cached)
units <- getUnitIndices(gi, chromosome="X")
nunits <- length(units)
cat(sprintf("Number of units on chromosome X: %d\n", nunits))
str(units)

# Plot the SNP density for this chromosome
plotDensity(gi, chromosome="X")

} # for (zzz in 0)
rm(zzz)


## End(Not run)

Gets the header of the CDF file

Description

Gets the header of the CDF file.

Usage

## S3 method for class 'AffymetrixCdfFile'
getHeader(this, ...)

Arguments

...

Not used.

Value

Returns a list structure as returned by readCdfHeader.

Gets the header of the CEL file

Description

Gets the header of the CEL file.

Usage

## S3 method for class 'AffymetrixCelFile'
getHeader(this, ...)

Arguments

...

Not used.

Value

Returns a list structure as returned by readCelHeader. If file does not exists, then NULL is returned.

Author(s)

Henrik Bengtsson

Gets the header of the PGF file

Description

Gets the header of the PGF file.

Usage

## S3 method for class 'AffymetrixPgfFile'
getHeader(this, ...)

Arguments

...

Not used.

Value

Returns a list structure as returned by readPgfHeader.

Gets the header of the annotation file

Description

Gets the header of the annotation file.

Usage

## S3 method for class 'AromaChipTypeAnnotationFile'
getHeader(...)

Arguments

...

Not used.

Value

Returns a list structure.

Gets the header of the CEL file

Description

Gets the header of the CEL file.

Usage

## S3 method for class 'CnagCfhFile'
getHeader(this, ...)

Arguments

...

Not used.

Value

Returns a list structure as returned by readCelHeader.

Creates an RGB Image object from a CEL file

Description

Creates an RGB Image object from a CEL file.

Usage

## S3 method for class 'AffymetrixCelFile'
getImage(this, other=NULL, transforms=list(sqrt), xrange=c(0, Inf), yrange=xrange,
  zrange=c(0, sqrt(2^16)), field=c("intensities", "stdvs", "pixels"), zoom=1, ...,
  readRectFcn=NULL, verbose=FALSE)

Arguments

other

An optional AffymetrixCelFile of the same chip type, that is used for calculating the ratio (non-logged). Note, to get the log-ratios, the log() function has to be specified as the first transform in the list of transformations.

xrange, yrange

vectors of length two specifying the (x0,x1) and (y0,y1) regions to be extracted. If NULL, the complete regions is used.

field

One of the CEL file fields, i.e. "intensities", stdvs, or pixels.

zoom

A numeric scale factor in (0,+Inf) for resizing the imaging. If 1, no resizing is done.

...

Additional arguments passed to *readRawDataRectangle() and more function.

readRectFcn

A function taking arguments 'xrange' and 'yrange', or NULL for the default read function.

verbose

A logical or a Verbose object.

Value

Returns an Image object as defined by the EBImage package. If palette==NULL, the color code is Grayscale, otherwise TrueColor.

Author(s)

Ken Simpson, Henrik Bengtsson

Gets the source data set

Description

Gets the source data set that is to be (or has been) transformed.

Usage

## S3 method for class 'TransformReport'
getInputDataSet(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCelSet.

Gets cell intensities from a set of cells and a set of arrays

Description

Gets cell intensities from a set of cells and a set of arrays.

Usage

## S3 method for class 'AffymetrixCelSet'
getIntensities(this, ...)

Arguments

...

Passed to *getData().

Value

Returns a numeric NxK matrix, where N is the number of cells read, and K is the number of arrays in the data set.

Author(s)

Henrik Bengtsson

Gets the name of the explorer

Description

Gets the name of the explorer.

Usage

## S3 method for class 'GenericReporter'
getName(this, ...)

Arguments

...

Not used.

Details

If a name alias has not been set explicitly, the input name will be used.

Value

Returns a character string.

Gets the name of the output data set

Description

Gets the name of the output data set, which is the same as the name of the input data set, unless an alias is set.

Usage

## S3 method for class 'Model'
getName(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the name of the output data set

Description

Gets the name of the output data set, which is the same as the input data set.

Usage

## S3 method for class 'TransformReport'
getName(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the transformed data set

Description

Gets the transformed data set, if processed.

Usage

## S3 method for class 'Transform'
getOutputDataSet(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

See Verbose.

Value

Returns an AromaMicroarrayDataSet or NULL.

Gets the transformed data set

Description

Gets the transformed data set, if processed.

Usage

## S3 method for class 'TransformReport'
getOutputDataSet(this, ...)

Arguments

...

Not used.

Value

Returns an AffymetrixCelSet.

Gets the path of this model

Description

Gets the path of this model where the parameter files are located. The directory is created, if missing.

Usage

## S3 method for class 'Model'
getPath(this, ...)

Arguments

...

Not used.

Details

If the path does not exist, it is created.

Value

Returns a character string.

Gets the path of the output data set

Description

Gets the path of the output data set. If non-existing, then the directory is created.

Usage

## S3 method for class 'TransformReport'
getPath(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the physical positions for a set of units

Description

Gets the physical positions for a set of units.

Usage

## S3 method for class 'GenomeInformation'
getPositions(this, ..., na.rm=FALSE)

Arguments

...

Arguments passed to *getData().

na.rm

If TRUE, non-defined unit indices are excluded, otherwise not.

Value

Returns an integer vector.

Gets the probe affinities for this model

Description

Gets the probe affinities for this model.

Usage

## S3 method for class 'ProbeLevelModel'
getProbeAffinityFile(this, ..., .class=ProbeAffinityFile)

Arguments

...

Not used.

.class

A ProbeAffinityFile class.

Value

Returns a ProbeAffinityFile object.

Calculates the residuals from a probe-level model

Description

Calculates the residuals from a probe-level model.

Usage

## S3 method for class 'QualityAssessmentModel'
getResiduals(this, units=NULL, path=NULL, name="qcData", tags="*", ram=NULL, force=FALSE,
  verbose=FALSE, ...)

Arguments

...

Additional arguments passed byPath() of QualityAssessmentSet.

Value

Returns an QualityAssessmentSet.

Gets the root path of this model

Description

Gets the root path of this model. By default, this is the string "model" appended by the capitalized name of the model class, e.g. "modelUnit".

Usage

## S3 method for class 'Model'
getRootPath(this, ...)

Arguments

...

Not used.

Value

Returns a character string.

Gets the names of the SNP units

Description

Gets the names of the SNP units.

Usage

## S3 method for class 'AffymetrixCdfFile'
getSnpNames(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

Gets the tags of the reporter

Description

Gets the tags of the reporter, which are the input tags plus additional tags.

Usage

## S3 method for class 'GenericReporter'
getTags(this, collapse=NULL, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Gets the tags of the output data set

Description

Gets the tags of the output data set, which consists of the tags of the input data set followed by an additional set of tags added by the model.

Usage

## S3 method for class 'Model'
getTags(this, collapse=NULL, ...)

Arguments

collapse

A character string used to concatenate the tags. If NULL, the tags are not concatenated.

...

Not used.

Value

Returns a character vector.

Gets the tags of the output data set

Description

Gets the tags of the output data set, which equals the tags of the input data set plus the tags of this transformation.

Usage

## S3 method for class 'TransformReport'
getTags(this, collapse=NULL, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Gets the timestamp in the CEL header

Description

Gets the timestamp in the CEL header.

Usage

## S3 method for class 'AffymetrixCelFile'
getTimestamp(this, format="%m/%d/%y %H:%M:%S", ...)

Arguments

format

The default format string for parsing the time stamp.

...

Not used.

Value

Returns a POSIXct object. The parsed string containing the timestamp is returned as attribute text.

Author(s)

Henrik Bengtsson

Gets a (unit, group, cell) index map

Description

Gets a (unit, group, cell) index map.

Usage

## S3 method for class 'ChipEffectFile'
getUnitGroupCellMap(this, units=NULL, force=FALSE, ..., verbose=FALSE)

Arguments

units

The units for which the map should be returned. If NULL, all units are considered.

force

If TRUE, cached cell indices are ignored.

...

Not used.

verbose

See Verbose.

Value

Returns a data.frame with integer columns unit, group, and cell.

Examples

## Not run: 
     unit group cell
   1  104     1  335
   2  104     2  336
   3  105     1  337
   4  105     2  338
   5  105     3  339
   6  105     4  340

## End(Not run)

Gets unit indices ordered along the chromosome

Description

Gets unit indices ordered along the chromosome.

Usage

## S3 method for class 'GenomeInformation'
getUnitIndices(this, ..., na.rm=TRUE)

Arguments

...

Arguments passed to *getData().

na.rm

If TRUE, non-defined unit indices are excluded, otherwise not.

Value

Returns an integer vector.

Gets cell signals for a subset of units and a subset of arrays

Description

Gets cell signals for a subset of units and a subset of arrays.

Usage

## S3 method for class 'AffymetrixCelSet'
getUnitIntensities(this, units=NULL, ..., force=FALSE, cache=!is.null(units),
  verbose=FALSE)

Arguments

units

An integer index vector specifying units to be read. If NULL, all units are read.

...

Arguments passed to the low-level function for reading CEL units, i.e. readCelUnits. If units is not already a CDF list structure, these arguments are also passed to readUnits() of AffymetrixCdfFile.

force

If TRUE, cached values are ignored.

verbose

If TRUE, progress details are printed, otherwise not. May also be a Verbose object.

Value

Returns a named list structure.

Author(s)

Henrik Bengtsson

Gets the names of each unit

Description

Gets the names of each unit.

Usage

## S3 method for class 'AffymetrixCdfFile'
getUnitNames(this, units=NULL, ...)

Arguments

units

The units of interest. If NULL, all units are considered.

...

Not used.

Details

Once read from file, this information is cached in memory for efficiency. The cache can be cleared by calling gc(cdf).

Value

Returns a vector of character names.

Gets the names of each unit

Description

Gets the names of each unit.

Usage

## S3 method for class 'AffymetrixPgfFile'
getUnitNames(this, units=NULL, ...)

Arguments

units

The units of interest. If NULL, all units are considered.

...

Not used.

Details

Once read from file, this information is cached in memory for efficiency. The cache can be cleared by calling gc(pgf).

Value

Returns a vector of character names.

Gets the types of a set of units

Description

Gets the types of a set of units.

Usage

## S3 method for class 'AffymetrixCdfFile'
getUnitTypes(this, units=NULL, ..., force=FALSE, .cache=TRUE, verbose=FALSE)

Arguments

units

The units of interest. If NULL, all units are considered.

...

Not used.

Details

Once read from file, this information is cached in memory for efficiency. The cache can be cleared by calling gc(cdf).

Value

Returns a vector of integers.

Calculates the weights from the robust fit to a probe-level model

Description

Calculates the weights from the robust fit to a probe-level model.

Usage

## S3 method for class 'QualityAssessmentModel'
getWeights(this, path=NULL, name="qcData", tags="*", ..., ram=NULL, force=FALSE,
  verbose=FALSE)

Arguments

path

name

tags

...

ram

force

verbose

Value

Returns an QualityAssessmentSet.

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays

Description

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays of units on a certain chromosome.

Usage

## S3 method for class 'ChipEffectFile'
getXAM(this, other, chromosome, units=NULL, ..., verbose=FALSE)

Arguments

other

The second ChipEffectFile object used as the reference.

chromosome

(The chromosome for which results should be returned.

units

(The subset of units to be matched. If NULL, all units are considered.

...

Not used.

verbose

See Verbose.

Value

Returns a Nx3 matrix where N is the number of units returned. The names of the columns are X (physical position in a given chromosome), A (log-intensities) and M (log-ratios). The names of the rows are the unit indices (as indexed by the CDF). Note: The rows are ordered according to chromosomal position.

Author(s)

Henrik Bengtsson

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays

Description

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays of units on a certain chromosome.

Usage

## S3 method for class 'ChipEffectSet'
getXAM(this, other, chromosome, units=NULL, ..., verbose=FALSE)

Arguments

other

The second ChipEffectFile object used as the reference.

chromosome

(The chromosome for which results should be returned.

units

(The subset of units to be matched. If NULL, all units are considered.

...

Not used.

verbose

See Verbose.

Value

Author(s)

Henrik Bengtsson

Groups units by dimensions

Description

Groups units by dimensions.

Usage

## S3 method for class 'AffymetrixCdfFile'
groupUnitsByDimension(this, units=NULL, ..., sort=TRUE, verbose=FALSE)

Arguments

units

An optional integer vector specifying the units to be queried.

...

Not used.

sort

If TRUE, the sets are ordered by number of groups per units and then by the number of cells per group.

verbose

A logical or Verbose.

Value

Returns a named list.

Author(s)

Henrik Bengtsson

Displays all or a subset of the data spatially

Description

Displays all or a subset of the data spatially.

Usage

## S3 method for class 'AffymetrixCelFile'
image270(this, xrange=c(0, Inf), yrange=c(0, Inf), takeLog=TRUE, interleaved=FALSE, ...,
  field=c("intensities", "stdvs", "pixels"), col=gray.colors(256), main=getName(this))

Arguments

xrange

A numeric vector of length two giving the left and right coordinates of the cells to be returned.

yrange

A numeric vector of length two giving the top and bottom coordinates of the cells to be returned.

...

Additional arguments passed image and [...].

field

The data field to be displayed.

col

The color map to be used.

main

The main title of the plot.

Value

Returns the (270-degrees rotated) data matrix.

Author(s)

Henrik Bengtsson

Identifies duplicated CEL files

Description

Identifies duplicated CEL files by comparing the timestamps in the CEL headers.

Usage

## S3 method for class 'AffymetrixCelSet'
isDuplicated(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

If TRUE, progress details are printed, otherwise not. May also be a Verbose object.

Value

Returns a logical vector of length equal to the number of files in the set. An element with value TRUE indicates that the corresponding CEL file has the same time stamp as another preceeding CEL file.

Author(s)

Henrik Bengtsson

Identifies duplicated CFH files

Description

Identifies duplicated CFH files by comparing the timestamps in the CFH headers.

Usage

## S3 method for class 'CnagCfhSet'
isDuplicated(this, ...)

Arguments

...

Not used.

Value

Returns a logical vector of length equal to the number of files in the set. An element with value TRUE indicates that the corresponding CFH file has the same time stamp as another preceeding CFH file.

Checks which cells (probes) are PMs and not

Description

Checks which cells (probes) are PMs and not.

Usage

## S3 method for class 'AffymetrixCdfFile'
isPm(this, units=NULL, force=FALSE, cache=TRUE, ..., verbose=FALSE)

Arguments

units

The units to be read. If NULL, all units are read.

...

Additional arguments passed to readCdfUnits.

force

If TRUE, cached results are ignored.

cache

If TRUE, results are cached.

verbose

A logical or Verbose.

Value

Returns a logical vector of length K, where K equals the total number of cells in the requested units. Note that the cells are ordered as they occur in the units, that is, not in incremental order.

Caching

This method caches a logical vector of length N, when N equals the number of cells on the array. The size of this vector is approximately 4*N bytes. The vector indicates if a cell is a PM or not.

Static method to check if a CDF is for a resequencing (CustomSeq) chip

Description

Static method to check if a CDF is for a resequencing (CustomSeq) chip. Note, this method is not bullet proof. Several resequencing CDF does not carry that information. For such, we add tests based on their chip type, as we become aware of them.

Usage

## S3 method for class 'AffymetrixCdfFile'
isResequenceChip(this, ...)

Arguments

...

Not used.

Value

Returns TRUE if the chip type refers to a resequence array, otherwise FALSE.

Author(s)

Henrik Bengtsson

Static method to check if a chip is a mapping (SNP) chip

Description

Static method to check if a chip is a mapping (SNP) chip.

Usage

## S3 method for class 'AffymetrixCdfFile'
isSnpChip(this, ...)

Arguments

...

Not used.

Value

Returns TRUE if the chip type refers to a SNP array, otherwise FALSE.

Author(s)

Henrik Bengtsson

Robust Multichip Analysis (RMA) reproducing the affy package

Description

Robust Multichip Analysis (RMA) reproducing the affy package as far as possible. The RMA method is described in [1].

The algorithm is processed in bounded memory, meaning a very large number of arrays can be analyzed on also very limited computer systems. The only limitation is the amount of memory required to load the final chip-effect estimates into memory (as a ExpressionSet).

Usage

  ## S3 method for class 'AffymetrixCelSet'
justRMA(csR, flavor=c("oligo", "affyPLM"), ..., verbose=FALSE)
  ## Default S3 method:
justRMA(...)

Arguments

csR

An AffymetrixCelSet.

flavor

A character string specifying the estimators used in the RMA summarization step.

...

Additional arguments passed to doRMA() used internally.

verbose

See Verbose.

Value

Returns an annotated ExpressionSet.

Reproducibility of affy

This implementation of the RMA method reproduces justRMA in affy package quite well. It does so by still using a constant memory profile, i.e. it is possible to use this implementation to run RMA on a much large data set than what is possible with affy. At least 20-50 times more samples should be doable, if not more.

Author(s)

Henrik Bengtsson

References

[1] Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

Gets the number of groups in each unit

Description

Gets the number of groups in each unit.

Usage

## S3 method for class 'AffymetrixCdfFile'
nbrOfGroupsPerUnit(this, units=NULL, ..., force=FALSE, verbose=FALSE)

Arguments

units

The units of interest. If NULL, all units are considered.

...

Not used.

verbose

A logical or Verbose.

Details

Once read from file, this information is cached in memory for efficiency. The cache can be cleared by calling gc(cdf).

Value

Returns a vector of integers.

Author(s)

Henrik Bengtsson

Gets the number of SNPs

Description

Gets the number of SNPs.

Usage

## S3 method for class 'AffymetrixCdfFile'
nbrOfSnps(this, ...)

Arguments

...

Additional arguments passed to *getSnpNames().

Value

Returns an integer.

Author(s)

Henrik Bengtsson

Normalizes the probe intensities to a target empirical distribution

Description

Normalizes the probe intensities to a target empirical distribution.

Usage

## S3 method for class 'AffymetrixCelFile'
normalizeQuantile(this, path=file.path("normQuantile", getChipType(this)), xTarget,
  subsetToUpdate=NULL, typesToUpdate=NULL, ..., overwrite=FALSE, skip=!overwrite,
  verbose=FALSE)

Arguments

path

The path where to save the normalized data files.

xTarget

A numeric vector. The empirical distribution to which all arrays should be normalized to.

subsetToUpdate

The indices of the probes to be updated. If NULL, all are updated.

typesToUpdate

Types of probes to be updated. For more details, see argument types of identifyCells() for the AffymetrixCdfFile class.

...

Additional arguments passed to normalizeQuantile().

overwrite

If TRUE, already normalized arrays are overwritten, unless skipped, otherwise an error is thrown.

skip

If TRUE, the array is not normalized if it already exists.

verbose

See Verbose.

Value

Returns the normalized AffymetrixCelFile object.

Author(s)

Henrik Bengtsson, Ken Simpson

Normalizes samples to have the same empirical distribution

Description

Normalizes samples to have the same empirical distribution.

Usage

## S3 method for class 'AffymetrixCelSet'
normalizeQuantile(this, path=NULL, name="normQuantile", subsetToUpdate=NULL,
  typesToUpdate=NULL, xTarget=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate,
  ..., verbose=FALSE)

Arguments

path

The path where to save the normalized data files. If NULL, a default name is used.

name

The name of the normalized data set, which will also be part of the default path.

subsetToUpdate

The probes to be updated. If NULL, all probes are updated.

typesToUpdate

Types of probes to be updated.

xTarget

A numeric vector. The empirical distribution to which all arrays should be normalized to.

subsetToAvg

The probes to calculate average empirical distribution over. If a single numeric in (0,1), then this fraction of all probes will be used. If NULL, all probes are considered.

typesToAvg

Types of probes to be used when calculating the average empirical distribution. If "pm" and "mm" only perfect-match and mismatch probes are used, respectively. If "pmmm" both types are used.

...

Additional arguments passed to normalizeQuantile().

verbose

See Verbose.

Value

Returns a double vector.

Author(s)

Henrik Bengtsson

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type

Description

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type. Platform Design (PD) packages are also known as "pdInfo" packages.

Disclaimer: This is a user-contributed function.

Instead of using this method, we recommend to use writeCdf() for the AffyGenePDInfo class.

Usage

pdInfo2Cdf(pdpkg, celfile, overwrite=FALSE, verbose=TRUE, ...)

Arguments

pdpkg

A character string for an existing PD package.

celfile

The pathname to an auxiliary CEL for the same chip type.

overwrite

If TRUE, an existing CDF is overwritten, otherwise an exception is thrown.

verbose

A logical or Verbose.

...

Not used.

Value

Returns (invisibly) the pathname to CDF written. The CDF filename is generated from the name of the PD package.

Limitations

The information available in the PD package is limited and does not contain all information needed to populate a CDF file. In order to workaround these limitations, certain CDF entries are set to predefined/hardwired values. The 'pbase' and 'tbase' entries of the generated CDF file is hardwired to "T" and "A", respectively. Likewise, the 'groupdirection' entry is hardwired to "sense".

Author(s)

Maintained by Mark Robinson. Original code by Samuel Wuest. Code improvements by Henrik Bengtsson.

Plots a (merged or non-merged) list of boxplot.stats() elements

Description

Plots a (merged or non-merged) list of boxplot.stats() elements.

Usage

## S3 method for class 'list'
plotBoxplotStats(stats, ylim=NULL, outline=FALSE, las=2, ...)

Arguments

stats

A (merged or non-merged) list of boxplot.stats elements.

ylim, outline, las, ...

Arguments passed to bxp.

Value

Returns (invisibly) the merged boxplot.stats structure.

Author(s)

Elizabeth Purdom

Plots the density of the probe signals on the array

Description

Plots the density of the probe signals on the array.

Usage

## S3 method for class 'AffymetrixCelFile'
plotDensity(this, subset=NULL, types=NULL, ..., xlim=c(0, 16), xlab=NULL,
  ylab="density (integrates to one)", log=TRUE, annotate=TRUE, verbose=FALSE)

Arguments

subset

The subset of probes to considered before any filtering by probe type is applied. If a vector of doubles, the cell indices. If a scalar double in [0,1], the fraction of cells, which can be used to speed up the plotting if approximate densities are acceptable. if NULL, all cells are considered.

types

The type of probes to include, e.g. "all", "pmmm", "pm", and "mm".

...

Additional arguments passed to plotDensity.numeric.

xlim

The range on the x axis.

xlab, ylab

The labels on the x and the y axes.

log

If TRUE, the density of the log (base 2) values are used, otherwise the non-logged values.

verbose

A logical or a Verbose object.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Plots the densities of all samples

Description

Plots the densities of all samples.

Usage

## S3 method for class 'AffymetrixCelSet'
plotDensity(this, subset=NULL, types=NULL, ..., col=seq_along(this), lty=NULL, lwd=NULL,
  annotate=TRUE, add=FALSE, verbose=FALSE)

Arguments

subset

types

The type of probes to include, e.g. "all", "pmmm", "pm", and "mm".

...

Additional arguments passed to plotDensity.AffymetrixCelFile().

col

A vector of colors for each of the arrays.

lty

A vector of line types for each of the arrays.

lwd

A vector of line widths for each of the arrays.

add

If FALSE, a new plot is created, otherwise the generated graphics is added to the current plot.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Plots the density of SNPs for a given chromosome

Description

Plots the density of SNPs for a given chromosome.

Usage

## S3 method for class 'GenomeInformation'
plotDensity(this, chromosome, ..., adjust=1/20, xlab=NULL, main=NULL, annotate=TRUE)

Arguments

chromosome

The chromsome to be displayed.

...

Additional arguments passed to *getPositions().

adjust

A bandwidth parameter for the density estimator.

xlab

The label on the x-axis. If NULL, a default will generated.

main

The title of the plot. If NULL, a default will generated.

annotate

If TRUE, the plot is annotated with extra information.

Value

Returns (invisibly) the estimated density.

Displays a spatial plot of a CEL file

Description

Displays a spatial plot of a CEL file.

Usage

## S3 method for class 'AffymetrixCelFile'
plotImage(this, ...)

Arguments

...

Arguments passed to *getImage().

Value

Returns (invisibly) the image displayed.

Author(s)

Ken Simpson, Henrik Bengtsson

Plots log-ratio versus log-intensity in a scatter plot

Description

Plots log-ratio versus log-intensity in a scatter plot.

Usage

## S3 method for class 'AffymetrixCelFile'
plotMvsA(this, reference, indices=NULL, pch=176, xlim=c(0, 16),
  ylim=c(-1, 1) * diff(xlim), xlab=expression(A == 1/2 %*% log[2](y[1] * y[2])),
  ylab=expression(M == log[2](y[1]/y[2])), ..., annotate=TRUE)

Arguments

reference

The reference channel, i.e. the denominator in the log ratios.

indices

Indices of the probe signals to be plotted.

pch

The plot symbol.

xlim, ylim

The range of the x and the y axes.

xlab, ylab

The labels on the x and the y axes.

...

Additional arguments passed to plot().

annotate

If TRUE, the plot is annotated with information about the data plotted, otherwise not.

Value

Returns (invisibly) a data.frame with the plotted data in the first two columns.

Author(s)

Henrik Bengtsson

Plots log-ratio versus another variable in a scatter plot

Description

Plots log-ratio versus another variable in a scatter plot.

Usage

## S3 method for class 'AffymetrixCelFile'
plotMvsX(this, reference, x, indices=NULL, pch=176, ylim=c(-1, 1) * 2, ylab=NULL, ...,
  what=c("M", "A"), add=FALSE, annotate=!add)

Arguments

reference

The reference channel, i.e. the denominator in the log ratios.

x

The other variable. A double vector.

indices

Indices of the probe signals to be plotted.

pch

The plot symbol.

ylim

The range of the y axes.

ylab

The labels on the y axes.

...

Additional arguments passed to plot().

annotate

If TRUE, the plot is annotated with information about the data plotted, otherwise not.

Value

Returns (invisibly) a data.frame with the plotted data in the first two columns, and remaining data in the following columns.

Author(s)

Henrik Bengtsson

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'AbstractProbeSequenceNormalization'
process(this, ..., ram=NULL, force=FALSE, verbose=FALSE)

Arguments

...

Not used.

ram

A positive double scale factor specifying how much more memory to use relative to the default.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Author(s)

Henrik Bengtsson

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'AdditiveCovariatesNormalization'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to normalizeFragmentLength (only for advanced users).

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Author(s)

Henrik Bengtsson

Calibrates the data set

Description

Calibrates the data set.

Usage

## S3 method for class 'AllelicCrosstalkCalibration'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already calibrated is re-calibrated, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Generates image files, scripts and dynamic pages for the explorer

Description

Generates image files, scripts and dynamic pages for the explorer.

Usage

## S3 method for class 'ArrayExplorer'
process(this, arrays=NULL, ..., verbose=FALSE)

Arguments

arrays

An optional vector of arrays to be processed. If NULL, all arrays are considered.

...

Not used.

verbose

A logical or Verbose.

Value

Returns nothing.

Processes the data set

Description

Processes the data set.

Usage

## S3 method for class 'BackgroundCorrection'
process(...)

Arguments

...

Not used.

Value

Returns a double vector.

Author(s)

Henrik Bengtsson

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'ChipEffectGroupMerge'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'DChipQuantileNormalization'
process(this, ..., force=FALSE, skip=TRUE, verbose=FALSE)

Arguments

...

Arguments passed to normalizeQuantileSpline.numeric.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'FragmentEquivalentClassNormalization'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'FragmentLengthNormalization'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Additional arguments passed to normalizeFragmentLength (only for advanced users).

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'GcContentNormalization'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Performs background correction

Description

Performs background correction.

Usage

## S3 method for class 'GcRmaBackgroundCorrection'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

verbose

See Verbose.

Value

Returns the output data set.

Generates report

Description

Generates report.

Usage

## S3 method for class 'GenericReporter'
process(...)

Arguments

...

See subclasses.

Value

Returns nothing.

Performs background correction

Description

Performs background correction.

Usage

## S3 method for class 'LimmaBackgroundCorrection'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

verbose

See Verbose.

Value

Returns a double vector.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'MatNormalization'
process(this, ..., ram=NULL, force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Processes the data set

Description

Processes the data set.

Usage

## S3 method for class 'MatSmoothing'
process(this, ..., units=NULL, force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already processed is re-processed, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Performs background correction

Description

Performs background correction.

Usage

## S3 method for class 'OpticalBackgroundCorrection'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

verbose

See Verbose.

Value

Returns the output data set.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'QuantileNormalization'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Calibrates the data set

Description

Calibrates the data set.

Usage

## S3 method for class 'ReseqCrosstalkCalibration'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already calibrated is re-calibrated, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Performs background correction

Description

Performs background correction.

Usage

## S3 method for class 'RmaBackgroundCorrection'
process(this, ..., force=FALSE, verbose=FALSE)

Arguments

...

Not used.

verbose

See Verbose.

Value

Returns the output data set.

Author(s)

Henrik Bengtsson

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'ScaleNormalization'
process(this, ..., skip=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'ScaleNormalization3'
process(this, ..., skip=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Generates image files, scripts and dynamic pages for the explorer

Description

Generates image files, scripts and dynamic pages for the explorer.

Usage

## S3 method for class 'SpatialReporter'
process(this, ..., verbose=FALSE)

Arguments

...

Not used.

verbose

A logical or Verbose.

Value

Returns nothing.

Normalizes the data set

Description

Normalizes the data set.

Usage

## S3 method for class 'UnitTypeScaleNormalization'
process(this, ..., skip=FALSE, force=FALSE, verbose=FALSE)

Arguments

...

Not used.

force

If TRUE, data already normalized is re-normalized, otherwise not.

verbose

See Verbose.

Value

Returns a double vector.

Sets and resets the .Random.seed in the global environment

Description

Sets and resets the .Random.seed in the global environment.

Usage

 randomSeed(action=c("set", "advance", "reset", "get"), seed=NULL, kind=NULL, backup=TRUE)

Arguments

action

A character string specifying the action.

seed

Random seed to be set; only for action="set". If length(seed) == 1, then set.seed(seed) is used, otherwise .Random.seed is assigned the value.

kind

(optional) A character string specifying type of random number generator to use, cf. RNGkind().

backup

If TRUE, the previous (seed, kind) state is recorded such that it can be reset later.

Value

Returns a .Random.seed.

Author(s)

Henrik Bengtsson

Gets all or a subset of the fields in a CEL file

Description

Gets all or a subset of the fields in a CEL file for all or a subset of the cells.

Usage

## S3 method for class 'AffymetrixCelFile'
readRawData(this, indices=NULL, fields=c("xy", "intensities", "stdvs", "pixels"), ...,
  drop=FALSE, verbose=FALSE)

Arguments

indices

A numeric vector of cell indices. If NULL, all cells are considered.

fields

Names of fields to be retrieved.

...

Additional arguments passed to readCel.

drop

If TRUE and a single field is returned, then data is returned as a vector, otherwise as a data.frame.

verbose

A logical or Verbose.

Value

Returns a data.frame of the fields requested (unless dimension dropped).

Caching

Neither in-memory nor on-file caching is done by this method.

Author(s)

Henrik Bengtsson

Reads CDF data unit by unit

Description

Reads CDF data unit by unit for all or a subset of units (probeset).

Usage

## S3 method for class 'AffymetrixCdfFile'
readUnits(this, units=NULL, ..., verbose=FALSE)

Arguments

units

The units to be read. If NULL, all units are read.

...

Additional arguments passed to readCdfUnits.

verbose

A logical or Verbose.

Value

Returns the list structure that readCdfUnits returns (possibly restructured).

Caching

CDF data is neither cached in memory nor on file by this method.

Reads CEL data unit by unit

Description

Reads CEL data unit by unit for all or a subset of units (probeset).

Usage

## S3 method for class 'AffymetrixCelFile'
readUnits(this, units=NULL, cdf=NULL, ..., stratifyBy=NULL, force=FALSE, cache=FALSE,
  verbose=FALSE)

Arguments

units

The units to be read. If NULL, all units are read.

cdf

An alternative CDF structure to be used. This overrides the units arguments.

...

Arguments passed to getUnits() of the AffymetrixCdfFile class (if cdf was not specified), but also to the readCelUnits methods.

Value

Returns the list structure that readCelUnits returns.

Caching

CEL data is neither cached in memory nor on file by this method.

Author(s)

Henrik Bengtsson

Reads CEL data unit by unit

Description

Reads CEL data unit by unit for all or a subset of units (probeset).

Usage

## S3 method for class 'CnagCfhFile'
readUnits(this, units=NULL, ..., verbose=FALSE)

Arguments

units

The units to be read. If NULL, all units are read.

...

Arguments passed to getUnits() of the AffymetrixCdfFile class (if cdf was not specified), but also to the readCelUnits methods.

Value

Returns the list structure that readCelUnits returns.

Caching

CEL data is neither cached in memory nor on file by this method.

Reads data unit by unit

Description

Reads data unit by unit for all or a subset of units (probeset) specially structured for this PLM.

Usage

## S3 method for class 'MultiArrayUnitModel'
readUnits(this, units=NULL, ..., verbose=FALSE)

Arguments

units

The units to be read. If NULL, all units are read.

...

Arguments passed to getCellIndices() of the AffymetrixCdfFile class (if cdf was not specified), but also to the readUnits() method of the AffymetrixCelSet class.

Value

Returns the list structure that readUnits() of AffymetrixCelSet returns.

Reads data unit by unit

Description

Reads data unit by unit for all or a subset of units (probeset) specially structured for this PLM.

Usage

## S3 method for class 'SingleArrayUnitModel'
readUnits(this, array, units=NULL, ..., verbose=FALSE)

Arguments

units

The units to be read. If NULL, all units are read.

...

Arguments passed to getCellIndices() of the AffymetrixCdfFile class (if cdf was not specified), but also to the readUnits() method of the AffymetrixCelFile class.

Value

Returns the list structure that readUnits() of AffymetrixCelFile returns.

Gets the cell quartets for each base position

Description

Gets the cell quartets for each base position.

Usage

## S3 method for class 'AffymetrixCdfFile'
readUnitsByQuartets(this, units=NULL, ..., verbose=FALSE)

Arguments

units

Subset of units to be queried. If NULL, all units are used.

...

Not used.

Value

Returns a vector of factors.

Author(s)

Henrik Bengtsson

Sets the alias of the report

Description

Sets the alias of the report. If specified, the alias overrides the report name, which is used by default.

Usage

## S3 method for class 'GenericReporter'
setAlias(this, alias=NULL, ...)

Arguments

alias

A character string for the new alias of the report. The alias must consists of valid filename characters, and must not contain commas, which are used to separate tags.

...

Not used.

Value

Returns nothing.

Sets the name alias for the model

Description

Sets the name alias for the model, if set.

Usage

## S3 method for class 'Model'
setAlias(this, alias=NULL, ...)

Arguments

alias

A character string, or NULL.

...

Not used.

Value

Returns nothing.

Sets the arrays

Description

Sets the arrays to be processed by the explorer.

Usage

## S3 method for class 'ArrayExplorer'
setArrays(this, ...)

Arguments

...

Not used.

Value

Returns a character vector.

Sets the CDF structure for this CEL file

Description

Sets the CDF structure for this CEL file.

Usage

## S3 method for class 'AffymetrixCelFile'
setCdf(this, cdf, ..., .checkArgs=TRUE)

Arguments

cdf

An AffymetrixCdfFile object.

...

Not used.

.checkArgs

(Internal) If FALSE, arguments are not validated.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Sets the CDF structure for this CEL set

Description

Sets the CDF structure for this CEL set. This structures is assigned to all CEL files in the set.

Usage

## S3 method for class 'AffymetrixCelSet'
setCdf(this, cdf, verbose=FALSE, ..., .checkArgs=TRUE)

Arguments

cdf

An AffymetrixCdfFile object.

verbose

If TRUE, progress details are printed, otherwise not. May also be a Verbose object.

...

Not used.

.checkArgs

(Internal) If FALSE, arguments are not validated.

Value

Returns nothing.

Author(s)

Henrik Bengtsson

Sets the CDF structure for this CEL file

Description

Sets the CDF structure for this CEL file.

Usage

## S3 method for class 'CnagCfhFile'
setCdf(this, cdf, ..., .checkArgs=TRUE)

Arguments

cdf

An AffymetrixCdfFile object.

...

Not used.

Value

Returns nothing.

Sets the CDF structure for this CFH set

Description

Sets the CDF structure for this CFH set. This structures is assigned to all CFH files in the set.

Usage

## S3 method for class 'CnagCfhSet'
setCdf(this, cdf, verbose=FALSE, ...)

Arguments

cdf

An AffymetrixCdfFile object.

...

Not used.

Value

Returns nothing.

Specifies a function through which

Description

Specifies a function through which of all or a subset of the units.

Usage

## S3 method for class 'AffymetrixCdfFile'
setRestructor(this, fcn=NULL, ...)

Arguments

...

Additional arguments passed to readCdfCellIndices.

Value

Returns the list structure returned by readCdfCellIndices.

Requirements

The reconstructor function have to:

Accept a list structure as its first argument.
Require no other arguments.
Return a list structure of identical length as the input one. In other words, it must not change the number of units nor the order of units.

The reconstructor function may:

Rearrange the groups or change the number of groups, for instance by utilizing applyCdfGroups.
Exclude some cells, for instance by excluding MMs.

Sets the tags to be appended

Description

Sets the tags to be appended to the tags of the input data set.

Usage

## S3 method for class 'Model'
setTags(this, tags=NULL, ...)

Arguments

tags

A character vector of tags. The tags may also be passed as comma-separated strings.

...

Not used.

Value

Returns nothing.

Setups example data in the current directory

Description

Setups example data in the current directory.

Usage

## S3 method for class 'AromaAffymetrix'
setupExampleData(pkg, dataset=NULL, chipType=NULL, dirs=c("annotationData", "rawData"),
  mustWork=TRUE, validate=FALSE, ...)

Arguments

dataset, chipType

character strings specifying the data set and the chip type to install.

dirs

A character vector specifying which directories to setup.

mustWork

If TRUE, an error is thrown if the requested data set could not be installed, otherwise not.

validate

If TRUE, the installed files are also validated, otherwise not.

...

Not used.

Value

Returns (invisibly) TRUE if all requested data was installed, otherwise FALSE.

Author(s)

Henrik Bengtsson

Plots log-ratio versus log-intensity in a smooth scatter plot

Description

Plots log-ratio versus log-intensity in a smooth scatter plot.

Usage

## S3 method for class 'AffymetrixCelFile'
smoothScatterMvsA(this, reference, indices=NULL, pch=176, xlim=c(0, 16),
  ylim=c(-1, 1) * diff(xlim), xlab=expression(A == 1/2 %*% log[2](y[1] * y[2])),
  ylab=expression(M == log[2](y[1]/y[2])), ..., annotate=TRUE)

Arguments

reference

The reference channel, i.e. the denominator in the log ratios.

indices

Indices of the probe signals to be plotted.

pch

The plot symbol.

xlim, ylim

The range of the x and the y axes.

xlab, ylab

The labels on the x and the y axes.

...

Additional arguments passed to plot().

annotate

If TRUE, the plot is annotated with information about the data plotted, otherwise not.

Value

Returns (invisibly) a data.frame with the plotted data in the first two columns.

Author(s)

Henrik Bengtsson

Updates CEL data unit by unit

Description

Updates CEL data unit by unit for all or a subset of units.

Usage

## S3 method for class 'AffymetrixCelFile'
updateUnits(this, data, ...)

Arguments

data

A list structure consisting of grouped data similar to what *readUnits() returns.

...

Not used.

Value

Returns the list structure that updateCelUnits returns.

Author(s)

Henrik Bengtsson

Verifies the correctness of the underlying file

Description

Verifies the correctness of the underlying file.

Usage

## S3 method for class 'GenomeInformation'
verify(this, ...)

Arguments

...

Not used.

Value

Returns (visibly) TRUE if the file is valid, otherwise an error is thrown.

Verifies the correctness of the underlying file

Description

Verifies the correctness of the underlying file.

Usage

## S3 method for class 'SnpInformation'
verify(this, ...)

Arguments

...

Not used.

Value

Returns (visibly) TRUE if the file is valid, otherwise an error is thrown.

Generates an Affymetrix CDF file from a Platform Design (PD) package

Description

Generates an Affymetrix CDF file from a Platform Design (PD) package. Platform Design (PD) packages are also known as "pdInfo" packages.

Usage

## S3 method for class 'AffyGenePDInfo'
writeCdf(this, tags=c("*"), unitsBy=c("transcript", "exon"), namesBy=c("fsetid", "id"),
  path=NULL, overwrite=FALSE, verbose=TRUE, ...)

Arguments

tags

An optional character vector of tags to be added to the CDF filename.

unitsBy

A character string specifying how to group units.

path

The output path where the CDF file is written. If NULL (default), then it is written to the corresponding annotationData/chipTypes/<chipType>/ directory.

overwrite

If TRUE, an existing CDF is overwritten, otherwise an exception is thrown.

verbose

A logical or Verbose.

...

Not used.

Details

The formal chip type of the CDF is inferred from the AffyGenePDInfo package. The filename of the CDF is constructed from the chip type and any optional tags. To minimize the risk for a corrupt CDF file, the creation of the file is atomic by first writing to a temporary file which is then renamed.

Value

Returns (invisibly) the pathname to CDF written.

Limitations

Author(s)

Henrik Bengtsson and Guido Hooiveld adopted from pdInfo2Cdf() written by Samuel Wuest and Mark Robinson.

Writes a spatial image of the signals in the CEL file

Description

Writes a spatial image of the signals in the CEL file.

Usage

## S3 method for class 'AffymetrixCelFile'
writeImage(this, filename=NULL, fullname=NULL, tags=c("*", "sqrt", "gray"),
  imgFormat="png", path=NULL, field=c("intensities", "stdvs", "pixels"), ..., skip=TRUE,
  verbose=FALSE)

Arguments

filename

A character string specifying the filename of the output file.

fullname

A character string specifying the full name of the output file.

tags

A character vector of optional tags added to the already existing tags of the CEL file.

imgFormat

A character string specifying the filename extension which also defines the image file format.

path

The path where the image file is stored.

...

Arguments passed to *getImage().

verbose

A logical or a Verbose object.

Value

Returns the pathname to the image file created.

Author(s)

Ken Simpson, Henrik Bengtsson

Examples

## Not run: 
  yellow.colors <- function(n) { hsv(h=0.15, v=0:(n-1)/(n-1)) }
  df <- ds[[1]]
  writeImage(df, tags="gray", palette=gray.colors(256), xrange=c(0,200))
  writeImage(df, tags="yellow", palette=yellow.colors(256), xrange=c(0,200))
  writeImage(df, tags="heat", palette=heat.colors(256), xrange=c(0,200))
  writeImage(df, tags="terrain", palette=terrain.colors(256), xrange=c(0,200))
  writeImage(df, tags="topo", palette=topo.colors(256), xrange=c(0,200))
  writeImage(df, tags="cm", palette=cm.colors(256), xrange=c(0,200))
  writeImage(df, tags="rainbow", palette=rainbow(256), xrange=c(0,200))

## End(Not run)

Package aroma.affymetrix

Description

Installation and updates

To get started

How to cite this package

License

Author(s)

References

The AbstractProbeSequenceNormalization class

Description

Usage

Arguments

Fields and Methods

Requirements

Author(s)

The AdditiveCovariatesNormalization class

Description

Usage

Arguments

Details

Fields and Methods

Author(s)

The AffineCnPlm class

Description

Usage

Arguments

Fields and Methods

Author(s)

The AffinePlm class

Description

Usage

Arguments

Fields and Methods

Model

Author(s)

References

The AffineSnpPlm class

Description

Usage

Arguments

Fields and Methods

Author(s)

The AffymetrixCdfFile class

Description

Usage

Arguments

Fields and Methods

Author(s)

Locates a CDF file from its chip type

Description

Usage

Arguments

Value

See Also

Defines an AffymetrixCdfFile object from a CDF file

Description

Usage

Arguments

Value

See Also

The AffymetrixCelFile class

Description

Usage

Arguments

Fields and Methods

For developers

Author(s)

See Also

Creates an empty CEL file from a template CDF

Description

Usage

Arguments

Value

Author(s)

See Also

Clears all or a subset of the fields in a CEL file

Description

Usage

Arguments

Value