SNPRelate : Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Package: SNPRelate
Type: Package
Title: Parallel Computing Toolset for Relatedness and Principal
Component Analysis of SNP Data
Version: 1.6.4
Date: 2016-06-14
Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
LinkingTo: gdsfmt
Suggests: parallel, RUnit, knitr, MASS, BiocGenerics
Enhances: SeqArray (>= 1.11.12)
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
NeedsCompilation: yes
Packaged: 2016-06-15 04:42:52 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>