DOI: 10.18129/B9.bioc.gdsfmt  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see gdsfmt.

R Interface to CoreArray Genomic Data Structure (GDS) Files

Bioconductor version: 3.16

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>

Citation (from within R, enter citation("gdsfmt")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


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


biocViews DataImport, Infrastructure, Software
Version 1.34.1
In Bioconductor since BioC 3.0 (R-3.1) (8.5 years)
License LGPL-3
Depends R (>= 2.15.0), methods
Suggests parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics
Depends On Me bigmelon, GDSArray, SAIGEgds, SCArray, SeqArray, SNPRelate
Imports Me CNVRanger, GBScleanR, GENESIS, ggmanh, GWASTools, SeqSQC, SeqVarTools, VariantExperiment
Suggests Me AnnotationHub, HIBAG
Links To Me SeqArray, SNPRelate
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