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>

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	1.14.1
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 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_1.14.1.tar.gz
Windows Binary	gdsfmt_1.14.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	gdsfmt_1.14.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gdsfmt
Package Short Url	http://bioconductor.org/packages/gdsfmt/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive