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 |
| 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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