To install this package, start R and enter:

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

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

gdsfmt

 

   

R Interface to CoreArray Genomic Data Structure (GDS) Files

Bioconductor version: Release (3.4)

This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with 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 of 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 available with relatively efficient random access. It is also 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), xz contributors (for the included liblzma sources)

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

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

Installation

To install this package, start R and enter:

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

Documentation

HTML R Script Introduction to GDS Format
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Infrastructure, Software
Version 1.10.0
In Bioconductor since BioC 3.0 (R-3.1) (2 years)
License LGPL-3
Depends R (>= 2.15.0)
Imports methods
LinkingTo
Suggests parallel, digest, crayon, RUnit, knitr, BiocGenerics
SystemRequirements
Enhances
URL http://corearray.sourceforge.net/ http://github.com/zhengxwen/gdsfmt
BugReports http://github.com/zhengxwen/gdsfmt/issues
Depends On Me bigmelon, SeqArray, SNPRelate
Imports Me GENESIS, GWASTools, SeqVarTools
Suggests Me HIBAG
Build Report  

Package Archives

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

Package Source gdsfmt_1.10.0.tar.gz
Windows Binary gdsfmt_1.10.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) gdsfmt_1.10.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/gdsfmt/tree/release-3.4
Package Short Url http://bioconductor.org/packages/gdsfmt/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: