gdsfmt

R Interface to CoreArray Genomic Data Structure (GDS) Files

Bioconductor version: Release (3.1)

This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers with less than 8 bits, since a single genetic/genomic variant, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are also supported with relatively efficient random access. It is allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

Author: Xiuwen Zheng [aut, cre], Stephanie Gogarten [ctb], Jean-loup Gailly and Mark Adler [ctb] (for the included zlib sources), Yann Collet [ctb] (for the included LZ4 sources)

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

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("gdsfmt")

Documentation

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

browseVignettes("gdsfmt")

Details

Package Archives

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