| Type: | Package |
| Title: | Natural Abundance Correction of Mass Spectrometer Data |
| Version: | 0.3.1 |
| Description: | An isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Supports correction for 13C, 2H and 15N. Su X, Lu W and Rabinowitz J (2017) <doi:10.1021/acs.analchem.7b00396>. |
| URL: | https://github.com/XiaoyangSu/AccuCor |
| BugReports: | https://github.com/XiaoyangSu/AccuCor/issues |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| Imports: | nnls, dplyr, stringr, readxl, readr, rlang, tibble, writexl, CHNOSZ |
| RoxygenNote: | 7.2.3 |
| Suggests: | testthat |
| NeedsCompilation: | no |
| Packaged: | 2023-09-14 14:08:53 UTC; lparsons |
| Author: | Xiaoyang Su  [aut],
Lance Parsons
[aut, cre],
Yujue Wang [ctb],
Princeton University [cph] |
| Maintainer: | Lance Parsons <lparsons@princeton.edu> |
| Repository: | CRAN |
| Date/Publication: | 2023-09-14 15:30:05 UTC |
accucor: A package for natural abundance correction of mass spectrometer data
Description
AccuCor is an isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. AccuCor supports correction for 13C, 2H and 15N.
AccuCor functions
Author(s)
Maintainer: Lance Parsons lparsons@princeton.edu (ORCID)
Authors:
Xiaoyang Su xs137@rwjms.rutgers.edu (ORCID)
Other contributors:
Yujue Wang yw429@rwjms.rutgers.edu (ORCID) [contributor]
Princeton University [copyright holder]
See Also
Useful links:
Natural Abundance carbon isotope correction for one metabolite
Description
Natural Abundance carbon isotope correction for one metabolite
Usage
carbon_isotope_correction(
formula,
datamatrix,
label,
Resolution,
ResDefAt = 200,
purity = 0.99,
ReportPoolSize = TRUE
)
Arguments
formula |
String representing molecular formula |
datamatrix |
Matrix of abundances for each sample for each isotope |
label |
vector of integer labels |
Resolution |
For Exactive, the Resolution is 100000, defined at Mw 200 |
ResDefAt |
Resolution defined at (in Mw), e.g. 200 Mw |
purity |
Carbon 13 purity, default: 0.99 |
ReportPoolSize |
default: TRUE |
Value
Named list of matrices: 'Corrected', 'Normalized', 'PoolBeforeDF', and 'PoolAfterDF'.
Examples
## Not run:
carbon_isotope_correction(
formula = "C6H13O9P",
datamatrix = DataMatrix,
label = c(0, 1, 2, 3, 4, 5),
Resolution = 100000
)
## End(Not run)
Standardize data frame columns and data types
Description
Standardize data frame columns and data types
Usage
clean_data_frame(df, columns_to_skip = NULL)
Arguments
df |
Data frame to clean |
columns_to_skip |
Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names. |
Value
"cleaned" data.frame which with columns 'compound', 'formula', 'isotope_label', label_index', followed by columns for each sample
Natural Abundance deuterium isotope correction for one metabolite
Description
Natural Abundance deuterium isotope correction for one metabolite
Usage
deuterium_isotope_correction(
formula,
datamatrix,
label,
Resolution,
ResDefAt = 200,
purity = 0.99,
ReportPoolSize = TRUE
)
Arguments
formula |
String representing molecular formula |
datamatrix |
Matrix of abundances for each sample for each isotope |
label |
vector of integer labels |
Resolution |
For Exactive, the Resolution is 100000, defined at Mw 200 |
ResDefAt |
Resolution defined at (in Mw), e.g. 200 Mw |
purity |
Deuterium purity, default: 0.99 |
ReportPoolSize |
default: TRUE |
Value
Named list of matrices: 'Corrected', 'Normalized', 'PoolBeforeDF', and 'PoolAfterDF'.
Examples
## Not run:
deuterium_isotope_correction(
formula = "C6H13O9P",
datamatrix = DataMatrix,
label = c(0, 1),
Resolution = 100000
)
## End(Not run)
Natural Abundance correction for mass spectrometry data
Description
natural_abundance_correction returns the corrected and normalized
intensities of isotopically labeled mass spectrometry data. It was designed
to work with input data from
El-MAVEN and
MAVEN software.
Usage
natural_abundance_correction(
data,
sheet = NULL,
compound_database = NULL,
output_base = NULL,
output_filetype = "xlsx",
columns_to_skip = NULL,
resolution,
resolution_defined_at = 200,
purity = NULL,
report_pool_size_before_df = FALSE,
path = NULL
)
Arguments
data |
Path to input data file (xlsx, xls, csv, txt, or tsv) OR dataframe. If dataframe is specified, specify output_base to output files automatically written. |
sheet |
Name of sheet in xlsx file with columns 'compound', 'formula', 'isotopelabel', and one column per sample. Defaults to the first sheet. |
compound_database |
Path to compound database in csv format. Only used for classic MAVEN style input when formula is not specified. |
output_base |
Path to basename of output file, default is the basename of the input path. '_corrected' will be appended. If 'FALSE' then no output file is written. |
output_filetype |
Filetype of the output file, one of: 'xls', xlsx', 'csv', or 'tsv'. The default is 'xlsx'. |
columns_to_skip |
Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names. |
resolution |
For Exactive, the resolution is 100000, defined at Mw 200 |
resolution_defined_at |
Mw at which the resolution is defined, default 200 Mw |
purity |
Isotope purity, default: Carbon 0.99; Deuterium 0.98; Nitrogen 0.99 |
report_pool_size_before_df |
Report PoolSizeBeforeDF, default = FALSE |
path |
Deprecated. Specify path to input data file (alias for 'data'). |
Details
C13, H2, and N15 isotopes are supported. The isotopes are detected from the
isotopeLabel column of the input file. The expected label text is
C13-label-#. D-label-#. or N15-label-#. Parent
(unlabeled) compounds are specified by C12 PARENT.
Value
Named list of matrices: 'Corrected', 'Normalized', 'PoolBeforeDF', and 'PoolAfterDF'.
Examples
## Not run:
natural_abundance_correction("inst/extdata/C_Sample_Input_Simple.xlsx",
Resolution = 100000, ResDefAt = 200
)
## End(Not run)
Natural Abundance deuterium isotope correction for one metabolite
Description
Natural Abundance deuterium isotope correction for one metabolite
Usage
nitrogen_isotope_correction(
formula,
datamatrix,
label,
Resolution,
ResDefAt = 200,
purity = 0.99,
ReportPoolSize = TRUE
)
Arguments
formula |
String representing molecular formula |
datamatrix |
Matrix of abundances for each sample for each isotope |
label |
vector of integer labels |
Resolution |
For Exactive, the Resolution is 100000, defined at Mw 200 |
ResDefAt |
Resolution defined at (in Mw), e.g. 200 Mw |
purity |
Nitrogen purity, default: 0.99 |
ReportPoolSize |
default: TRUE |
Value
Named list of matrices: 'Corrected', 'Normalized', 'PoolBeforeDF', and 'PoolAfterDF'.
Examples
## Not run:
nitrogen_isotope_correction(
formula = "C23H38N7O17P3S",
datamatrix = DataMatrix,
label = c(0, 1, 2, 3, 4, 5, 6, 7),
Resolution = 140000
)
## End(Not run)
Natural Abundance correction for Carbon labeled samples
Description
Natural Abundance correction for Carbon labeled samples
Usage
read_elmaven(
path,
sheet = NULL,
compound_database = NULL,
columns_to_skip = NULL,
filetype = NULL,
...
)
Arguments
path |
Path to input file. |
sheet |
Name of sheet in xlsx file with columns 'compound', 'formula', 'isotopelabel', and one column per sample. Defaults to the first sheet. |
compound_database |
Path to compound database in csv format. Only used for classic MAVEN style input when formula is not specified. |
columns_to_skip |
Specify column heading to skip. All other columns not named 'compound', 'formula', and 'isotopelabel' will be assumed to be sample names. |
filetype |
Specify file type, default is to determine by file extension. |
... |
Pass additional parameters to readxl::read_excel |
Value
List containing three items: "original" data.frame which is result of read_excel, "cleaned" data.frame which with columns 'compound', 'formula', 'isotope_label', label_index', followed by columns for each sample, and "isotope" which is a character indicating the isotope
Examples
## Not run:
read_elmaven_xlsx("ExcelFile", "Sheet1")
## End(Not run)