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gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) files === [![Build Status](]( [![Build status](]( ## Features This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include 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 with less than 8 bits, since a single genetic/genomic variant, like single-nucleotide polymorphism, usually occupies fewer bits than a byte. Data compression and decompression are also supported with relatively efficient random access. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package. ## Bioconductor: Release Version: v1.2.2 []( Development Version: v1.3.10 []( ## Package Vignettes []( []( ## License ![LGPLv3]( [LGPL-3]( ## Citation Xiuwen Zheng, David Levine, Jess Shen, Stephanie M. Gogarten, Cathy Laurie, Bruce S. Weir. A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics 2012; [doi:10.1093/bioinformatics/bts606]( ## Package Maintainer Xiuwen Zheng ([]( ## URL []( ## Unit Testing Comprehensive unit testing: []( ## Installation * Bioconductor repository: ```R source("") biocLite("gdsfmt") ``` * Development version from Github: ```R library("devtools") install_github("zhengxwen/gdsfmt") ``` The `install_github()` approach requires that you build from source, i.e. `make` and compilers must be installed on your system -- see the [R FAQ]( for your operating system; you may also need to install dependencies manually. ## Copyright notice * CoreArray C++ library, LGPL-3 License, 2007-2015, Xiuwen Zheng * zlib, zlib License, 1995-2015, Jean-loup Gailly and Mark Adler * LZ4, BSD 2-clause License, 2011-2015, Yann Collet