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: 2.0-2
Depends: R (≥ 4.0.0)
Imports: haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, BiocStyle, poisbinom
Suggests: testthat, knitr, rmarkdown, biomaRt
Published: 2020-11-10
Author: Juan R Gonzalez and Victor Moreno
Maintainer: Juan R Gonzalez <juanr.gonzalez at isglobal.org>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://brge.isglobal.org
NeedsCompilation: no
In views: Genetics, MissingData
CRAN checks: SNPassoc results

Downloads:

Reference manual: SNPassoc.pdf
Vignettes: SNPassoc: an R package to perform whole genome association studies
Package source: SNPassoc_2.0-2.tar.gz
Windows binaries: r-devel: SNPassoc_2.0-2.zip, r-release: SNPassoc_2.0-2.zip, r-oldrel: not available
macOS binaries: r-release: SNPassoc_2.0-2.tgz, r-oldrel: not available
Old sources: SNPassoc archive

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