Package: SNPRelate
Type: Package
Title: Parallel Computing Toolset for Relatedness and Principal
        Component Analysis of SNP Data
Version: 1.16.0
Date: 2018-09-23
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"),
        person("Stephanie", "Gogarten", role="ctb"),
        person("Cathy", "Laurie", role="ctb"),
        person("Bruce", "Weir", role=c("ctb", "ths"),
        email="bsweir@u.washington.edu"))
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.
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_8
git_last_commit: 0e38e8d
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: yes
Packaged: 2018-10-31 00:22:08 UTC; biocbuild
Author: Xiuwen Zheng [aut, cre, cph],
  Stephanie Gogarten [ctb],
  Cathy Laurie [ctb],
  Bruce Weir [ctb, ths]
Maintainer: Xiuwen Zheng <zhengx@u.washington.edu>
Built: R 3.5.1; x86_64-conda_cos6-linux-gnu; 2018-12-10 09:31:27 UTC; unix
