SNPassoc: SNPs-Based Whole Genome Association Studies

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi:10.1093/bioinformatics/btm025>.

Version: 2.0-11
Depends: R (≥ 4.0.0)
Imports: haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, BiocStyle, poisbinom, Biostrings, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, GenomicRanges, IRanges, S4Vectors, org.Hs.eg.db
Suggests: testthat, knitr, rmarkdown, biomaRt, SNPlocs.Hsapiens.dbSNP144.GRCh38, MafDb.1Kgenomes.phase3.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, GenomicScores, BSgenome
Published: 2021-12-03
Author: Victor Moreno [aut], Juan R Gonzalez [aut, cre]
Maintainer: Juan R Gonzalez <juanr.gonzalez at isglobal.org>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/isglobal-brge/SNPassoc
NeedsCompilation: no
Materials: README
CRAN checks: SNPassoc results

Documentation:

Reference manual: SNPassoc.pdf
Vignettes: SNPassoc: an R package to perform whole genome association studies

Downloads:

Package source: SNPassoc_2.0-11.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-release (x86_64): SNPassoc_2.0-11.tgz, r-oldrel: SNPassoc_2.0-11.tgz
Old sources: SNPassoc archive

Linking:

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