To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

SNPRelate

   

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see SNPRelate.

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

Bioconductor version: 3.1

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 format in this package is also used by the GWASTools package with the support of S4 classes and generic functions.

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SNPRelate")

 

HTML R Script Tutorials for the R/Bioconductor Package SNPRelate
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 2.14), gdsfmt(>= 1.2.2)
Imports
LinkingTo gdsfmt
Suggests parallel, RUnit, knitr, MASS, BiocGenerics
SystemRequirements
Enhances
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
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source SNPRelate_1.2.0.tar.gz
Windows Binary SNPRelate_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SNPRelate_1.2.0.tgz
Mac OS X 10.9 (Mavericks) SNPRelate_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SNPRelate/tree/release-3.1
Package Short Url http://bioconductor.org/packages/SNPRelate/
Package Downloads Report Download Stats

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