Package: SNPRelate
Type: Package
Title: Parallel Computing Toolset for Relatedness and Principal
        Component Analysis of SNP Data
Version: 1.20.1
Date: 2019-11-21
Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
LinkingTo: gdsfmt
Imports: methods
Suggests: parallel, Matrix, RUnit, knitr, MASS, BiocGenerics
Enhances: SeqArray (>= 1.12.0)
Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre", "cph"),
        email="zhengx@u.washington.edu", comment=c(ORCID="0000-0002-1390-0708")),
        person("Stephanie", "Gogarten", role="ctb"),
        person("Cathy", "Laurie", role="ctb"),
        person("Bruce", "Weir", role=c("ctb", "ths"),
        email="bsweir@u.washington.edu", comment=c(ORCID="0000-0002-4883-1247")))
Description: Genome-wide association studies (GWAS) are widely used to investigate the
        genetic basis of diseases and traits, but they pose many computational
        challenges. We developed an R package SNPRelate to provide a binary format for
        single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic
        Data Structure (GDS) data files. The GDS format offers the efficient operations
        specifically designed for integers with two bits, since a SNP could occupy only
        two bits. SNPRelate is also designed to accelerate two key computations on SNP
        data using parallel computing for multi-core symmetric multiprocessing computer
        architectures: Principal Component Analysis (PCA) and relatedness analysis using
        Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools
        package with the support of S4 classes and generic functions. The extended GDS
        format is implemented in the SeqArray package to support the storage of single
        nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and
        structural variation calls in whole-genome and whole-exome variant data.
License: GPL-3
VignetteBuilder: knitr
URL: http://github.com/zhengxwen/SNPRelate,
        http://corearray.sourceforge.net/tutorials/SNPRelate/
BugReports: http://github.com/zhengxwen/SNPRelate/issues
biocViews: Infrastructure, Genetics, StatisticalMethod,
        PrincipalComponent
git_url: https://git.bioconductor.org/packages/SNPRelate
git_branch: RELEASE_3_10
git_last_commit: 210b76d
git_last_commit_date: 2019-11-22
Date/Publication: 2019-11-22
NeedsCompilation: yes
Packaged: 2019-11-23 03:28:25 UTC; biocbuild
Author: Xiuwen Zheng [aut, cre, cph] (<https://orcid.org/0000-0002-1390-0708>),
  Stephanie Gogarten [ctb],
  Cathy Laurie [ctb],
  Bruce Weir [ctb, ths] (<https://orcid.org/0000-0002-4883-1247>)
Maintainer: Xiuwen Zheng <zhengx@u.washington.edu>
Built: R 3.6.1; i386-w64-mingw32; 2019-11-23 15:23:20 UTC; windows
Archs: i386, x64
