SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data

Features

Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R package for multi-core symmetric multiprocessing computer architectures) to accelerate two key computations on SNP data: principal component analysis (PCA) and relatedness analysis using identity-by-descent measures. The kernels of our algorithms are written in C/C++ and highly optimized.

Bioconductor:

Release Version: v1.0.1

http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html

Development Version: v1.1.11

http://www.bioconductor.org/packages/devel/bioc/html/SNPRelate.html

Tutorials

http://corearray.sourceforge.net/tutorials/SNPRelate

http://www.bioconductor.org/packages/devel/bioc/vignettes/SNPRelate/inst/doc/SNPRelateTutorial.html

Citation

Xiuwen Zheng, David Levine, Jess Shen, Stephanie M. Gogarten, Cathy Laurie, Bruce S. Weir. A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics 2012; doi:10.1093/bioinformatics/bts606.

Installation

• Bioconductor repository:

source("http://bioconductor.org/biocLite.R")
biocLite("SNPRelate")

• Development version from Github:

library("devtools")
install_github("zhengxwen/gdsfmt")
install_github("zhengxwen/SNPRelate")

The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

• Install the package from the source code: gdsfmt, SNPRelate

wget --no-check-certificate https://github.com/zhengxwen/gdsfmt/tarball/master -O gdsfmt_latest.tar.gz
wget --no-check-certificate https://github.com/zhengxwen/SNPRelate/tarball/master -O SNPRelate_latest.tar.gz
## Or
curl -L https://github.com/zhengxwen/gdsfmt/tarball/master/ -o gdsfmt_latest.tar.gz
curl -L https://github.com/zhengxwen/SNPRelate/tarball/master/ -o SNPRelate_latest.tar.gz

## Install
R CMD INSTALL gdsfmt_latest.tar.gz
R CMD INSTALL SNPRelate_latest.tar.gz

• Old version (<=v0.9.19) from R-Forge repository:

install.packages("gdsfmt", repos="http://R-Forge.R-project.org")
install.packages("SNPRelate", repos="http://R-Forge.R-project.org")