SNPs-Based Whole Genome Association Studies R package SNPassoc version 2.3.1 CRAN Task View: MissingData (https://CRAN.R-project.org/view=MissingData) 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>. This version includes internal copies of functions from the archived 'haplo.stats' package to maintain functionality. Software Depends: R (>= 4.0.0) Imports: mvtnorm, parallel, survival, tidyr, plyr, ggplot2, poisbinom, rms, methods Suggests: testthat, knitr, rmarkdown, biomaRt, VariantAnnotation, GenomicRanges, IRanges, S4Vectors, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene Dolors Pelegri <dolors.pelegri@isglobal.org> Comprehensive R Archive Network (CRAN) Victor Moreno [aut], Juan R Gonzalez [aut] (ORCID: <https://orcid.org/0000-0003-3267-2146>), Dolors Pelegri [aut, cre] (ORCID: <https://orcid.org/0000-0002-5993-3003>) GPL (>= 2) 2026-04-13 application/tgz https://CRAN.R-project.org/package=SNPassoc doi:10.32614/CRAN.package.SNPassoc