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## try http:// if https:// URLs are not supported
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biocLite("SNPRelate")

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SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate    

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

Bioconductor version: Release (3.5)

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.

Author: Xiuwen Zheng [aut, cre, cph], Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths]

Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>

Citation (from within R, enter citation("SNPRelate")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPRelate")

Documentation

HTML R Script SNPRelate Tutorial
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod
Version 1.10.2
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License GPL-3
Depends R (>= 2.15), gdsfmt(>= 1.8.3)
Imports
LinkingTo gdsfmt
Suggests parallel, RUnit, knitr, MASS, BiocGenerics
SystemRequirements
Enhances SeqArray(>= 1.12.0)
URL http://github.com/zhengxwen/SNPRelate http://corearray.sourceforge.net/tutorials/SNPRelate/
BugReports http://github.com/zhengxwen/SNPRelate/issues
Depends On Me
Imports Me
Suggests Me GENESIS, GWASTools, HIBAG, SeqArray
Build Report  

Package Archives

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Package Source SNPRelate_1.10.2.tar.gz
Windows Binary SNPRelate_1.10.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SNPRelate_1.10.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/SNPRelate
Package Short Url http://bioconductor.org/packages/SNPRelate/
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