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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 (3.6)

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>

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


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


biocViews DataImport, Infrastructure, Software
Version 1.13.2
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License LGPL-3
Depends R (>= 2.15.0), methods
Suggests parallel, digest, crayon, RUnit, knitr, BiocGenerics
Depends On Me bigmelon, SeqArray, SNPRelate
Imports Me GENESIS, GWASTools, SeqVarTools
Suggests Me AnnotationHub, HIBAG
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