gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files
Version 1.12.0

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.

Package details

AuthorXiuwen 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)
Bioconductor views DataImport Infrastructure Software
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseLGPL-3
Version1.12.0
URL http://corearray.sourceforge.net/ http://github.com/zhengxwen/gdsfmt
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gdsfmt")

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gdsfmt documentation built on May 31, 2017, 3:12 p.m.