To install this package, start R and enter:

## try http if https is not available
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 (3.1)

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>

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

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")

 

HTML R Script R Interface to CoreArray Genomic Data Structure (GDS) Files
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Infrastructure, Software
Version 1.4.0
In Bioconductor since BioC 3.0 (R-3.1) (1 year)
License LGPL-3
Depends R (>= 2.14.0)
Imports methods
LinkingTo
Suggests parallel, 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 SeqArray, SNPRelate
Imports Me GWASTools, SeqVarTools
Suggests Me GENESIS, HIBAG
Build Report  

Package Archives

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

Package Source gdsfmt_1.4.0.tar.gz
Windows Binary gdsfmt_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) gdsfmt_1.4.0.tgz
Mac OS X 10.9 (Mavericks) gdsfmt_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/gdsfmt/tree/release-3.1
Package Short Url http://bioconductor.org/packages/gdsfmt/
Package Downloads Report Download Stats

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