gdsfmt

DOI: 10.18129/B9.bioc.gdsfmt    

This is the development version of gdsfmt; for the stable release version, see gdsfmt.

R Interface to CoreArray Genomic Data Structure (GDS) Files

Bioconductor version: Development (3.8)

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:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("gdsfmt", version = "devel")

Documentation

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

browseVignettes("gdsfmt")

 

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

Details

biocViews DataImport, Infrastructure, Software
Version 1.17.2
In Bioconductor since BioC 3.0 (R-3.1) (4 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, GDSArray, 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_1.17.2.tar.gz
Windows Binary gdsfmt_1.17.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) gdsfmt_1.17.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/gdsfmt
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gdsfmt
Package Short Url http://bioconductor.org/packages/gdsfmt/
Package Downloads Report Download Stats

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