To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("gdsfmt")

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

gdsfmt

DOI: 10.18129/B9.bioc.gdsfmt    

R Interface to CoreArray Genomic Data Structure (GDS) Files

Bioconductor version: Release (3.6)

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 diploid genotype, 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("http://bioc.ism.ac.jp/biocLite.R")
biocLite("gdsfmt")

Documentation

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

Details

biocViews DataImport, Infrastructure, Software
Version 1.14.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License LGPL-3
Depends R (>= 2.15.0), methods
Imports
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, SeqSQC, SeqVarTools
Suggests Me AnnotationHub, HIBAG
Build Report  

Package Archives

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

Source Package gdsfmt_1.14.0.tar.gz
Windows Binary gdsfmt_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) gdsfmt_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gdsfmt
Package Short Url http://bioconductor.org/packages/gdsfmt/
Package Downloads Report Download Stats

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