gdsfmt
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see gdsfmt.
R Interface to CoreArray Genomic Data Structure (GDS) Files
Bioconductor version: 3.9
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 <zhengxwen at gmail.com>
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")
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Follow Installation instructions to use this package in your R session.