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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: 2.1-2
Depends: R (≥ 4.0.0)
Imports: haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, poisbinom
Suggests: testthat, knitr, rmarkdown, biomaRt, VariantAnnotation, GenomicRanges, IRanges, S4Vectors, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
Published: 2024-10-28
DOI: 10.32614/CRAN.package.SNPassoc
Author: Victor Moreno [aut], Juan R Gonzalez ORCID iD [aut], Dolors Pelegri ORCID iD [aut, cre]
Maintainer: Dolors Pelegri <dolors.pelegri at isglobal.org>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/isglobal-brge/SNPassoc
NeedsCompilation: no
Materials: README
In views: MissingData
CRAN checks: SNPassoc results

Documentation:

Reference manual: SNPassoc.pdf
Vignettes: SNPassoc: an R package to perform whole genome association studies (source, R code)

Downloads:

Package source: SNPassoc_2.1-2.tar.gz
Windows binaries: r-devel: SNPassoc_2.1-2.zip, r-release: SNPassoc_2.1-2.zip, r-oldrel: SNPassoc_2.1-2.zip
macOS binaries: r-release (arm64): SNPassoc_2.1-2.tgz, r-oldrel (arm64): SNPassoc_2.1-2.tgz, r-release (x86_64): SNPassoc_2.1-2.tgz, r-oldrel (x86_64): SNPassoc_2.1-2.tgz
Old sources: SNPassoc archive

Reverse dependencies:

Reverse imports: dartR.base

Linking:

Please use the canonical form https://CRAN.R-project.org/package=SNPassoc to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.