gdsfmt

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see gdsfmt.

R Interface to CoreArray Genomic Data Structure (GDS) Files

Bioconductor version: 3.10

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 [ctb] (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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gdsfmt")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("gdsfmt")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, Software
Version	1.22.0
In Bioconductor since	BioC 3.0 (R-3.1) (9.5 years)
License	LGPL-3
Depends	R (>= 2.15.0), methods
Imports
System Requirements
URL	http://corearray.sourceforge.net/ http://github.com/zhengxwen/gdsfmt
Bug Reports	http://github.com/zhengxwen/gdsfmt/issues

Suggests	parallel, digest, crayon, RUnit, knitr, BiocGenerics
Linking To
Enhances
Depends On Me	bigmelon, GDSArray, SAIGEgds, SeqArray, SNPRelate
Imports Me	CNVRanger, GENESIS, GWASTools, SeqSQC, SeqVarTools, VariantExperiment
Suggests Me	AnnotationHub, HIBAG
Links To Me	SeqArray, SNPRelate
Build Report	Build Report

Package Archives

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

Source Package	gdsfmt_1.22.0.tar.gz
Windows Binary	gdsfmt_1.22.0.zip
Mac OS X 10.11 (El Capitan)	gdsfmt_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gdsfmt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gdsfmt
Bioc Package Browser	https://code.bioconductor.org/browse/gdsfmt/
Package Short Url	https://bioconductor.org/packages/gdsfmt/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive