SeqArray: Big Data Management of Genome-Wide Sequencing Variants

Features

Big data management of genome-wide variants using the CoreArray C++ library: genotypic data and annotations are stored in an array-oriented manner, offering efficient access of genetic variants using the S programming language.

Bioconductor:

Development Version: v1.7.5

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

Installation

• Bioconductor repository:

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

• Development version from Github:

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

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, SeqArray

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

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