gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) files === [](https://travis-ci.org/zhengxwen/gdsfmt) ## 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: Development Version: v1.3.2 [http://www.bioconductor.org/packages/devel/bioc/html/gdsfmt.html](http://www.bioconductor.org/packages/devel/bioc/html/gdsfmt.html) ## Package Vignettes [http://www.bioconductor.org/packages/devel/bioc/vignettes/gdsfmt/inst/doc/gdsfmt_vignette.pdf](http://www.bioconductor.org/packages/devel/bioc/vignettes/gdsfmt/inst/doc/gdsfmt_vignette.pdf) ## License  [LGPL-3](https://www.gnu.org/licenses/lgpl.html) ## 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](http://dx.doi.org/10.1093/bioinformatics/bts606) ## Package Maintainer Xiuwen Zheng ([zhengx@u.washington.edu](zhengx@u.washington.edu)) ## URL [http://github.com/zhengxwen/gdsfmt](http://github.com/zhengxwen/gdsfmt) ## Unit Testing Comprehensive unit testing: [http://github.com/zhengxwen/unittest.gdsfmt](http://github.com/zhengxwen/unittest.gdsfmt) ## Installation * Bioconductor repository: ```R source("http://bioconductor.org/biocLite.R") biocLite("gdsfmt") ``` * Development version from Github: ```R library("devtools") install_github("zhengxwen/gdsfmt") ``` ## 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