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README.md
gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) files === [![Build Status](https://travis-ci.org/zhengxwen/gdsfmt.png)](https://travis-ci.org/zhengxwen/gdsfmt) [![Build status](https://ci.appveyor.com/api/projects/status/6ussam0n65o32r0j?svg=true)](https://ci.appveyor.com/project/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: Release Version: v1.2.2 [http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html](http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html) Development Version: v1.3.10 [http://www.bioconductor.org/packages/devel/bioc/html/gdsfmt.html](http://www.bioconductor.org/packages/devel/bioc/html/gdsfmt.html) ## Package Vignettes [http://corearray.sourceforge.net/tutorials/gdsfmt/](http://corearray.sourceforge.net/tutorials/gdsfmt/) [http://www.bioconductor.org/packages/devel/bioc/vignettes/gdsfmt/inst/doc/gdsfmt_vignette.html](http://www.bioconductor.org/packages/devel/bioc/vignettes/gdsfmt/inst/doc/gdsfmt_vignette.html) ## License ![LGPLv3](http://www.gnu.org/graphics/lgplv3-88x31.png) [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") ``` 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](http://cran.r-project.org/faqs.html) 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