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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 (3.19)

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is 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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataImport, Infrastructure, Software
Version 1.39.3
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 https://github.com/zhengxwen/gdsfmt
Bug Reports https://github.com/zhengxwen/gdsfmt/issues
See More
Suggests parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics
Linking To
Enhances
Depends On Me bigmelon, GDSArray, RAIDS, SAIGEgds, SCArray, SeqArray, SNPRelate
Imports Me CNVRanger, GBScleanR, GENESIS, ggmanh, GWASTools, SCArray.sat, 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_1.39.3.tar.gz
Windows Binary gdsfmt_1.39.3.zip (64-bit only)
macOS Binary (x86_64) gdsfmt_1.39.3.tgz
macOS Binary (arm64)
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