Package: SNPRelate
Type: Package
Title: Parallel Computing Toolset for Relatedness and Principal
        Component Analysis of SNP Data
Version: 1.45.0
Date: 2025-09-26
Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
LinkingTo: gdsfmt
Imports: methods, RhpcBLASctl
Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, 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", email="sdmorris@uw.edu"),
        person("Cathy", "Laurie", role="ctb", email="cclaurie@uw.edu"),
        person("Bruce", "Weir", role=c("ctb", "ths"), email="bsweir@uw.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
LazyData: true
URL: https://github.com/zhengxwen/SNPRelate
BugReports: https://github.com/zhengxwen/SNPRelate/issues
biocViews: Infrastructure, Genetics, StatisticalMethod,
        PrincipalComponent
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:21:20 UTC
RemoteUrl: https://github.com/bioc/SNPRelate
RemoteRef: HEAD
RemoteSha: 3bd5f10ba8f0c298f6a1008351cf070012a76624
NeedsCompilation: yes
Packaged: 2025-10-30 11:27:22 UTC; root
Author: Xiuwen Zheng [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-1390-0708>),
  Stephanie Gogarten [ctb],
  Cathy Laurie [ctb],
  Bruce Weir [ctb, ths] (ORCID: <https://orcid.org/0000-0002-4883-1247>)
Maintainer: Xiuwen Zheng <zhengx@u.washington.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-30 11:29:19 UTC; windows
Archs: x64
