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README.md 100644 7 kb
README.md
gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) files === ![LGPLv3](http://www.gnu.org/graphics/lgplv3-88x31.png) [GNU Lesser General Public License, LGPL-3](https://www.gnu.org/licenses/lgpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/gdsfmt.svg)](http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/gdsfmt.svg)](http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html) [![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) [![Comparison is done across all Bioconductor packages over the last 6 months](http://www.bioconductor.org/shields/downloads/gdsfmt.svg)](http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html) [![codecov.io](https://codecov.io/github/zhengxwen/gdsfmt/coverage.svg?branch=master)](https://codecov.io/github/zhengxwen/gdsfmt?branch=master) ## Features 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. ## Bioconductor: Release Version: v1.26.0 [http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html](http://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html) [Help Documents](https://rdrr.io/bioc/gdsfmt/man) [News](./NEWS): v1.26.0 ## Package Vignettes [http://bioconductor.org/packages/release/bioc/vignettes/gdsfmt/inst/doc/gdsfmt.html](http://bioconductor.org/packages/release/bioc/vignettes/gdsfmt/inst/doc/gdsfmt.html) ## Citations Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. *Bioinformatics*. [DOI: 10.1093/bioinformatics/bts606](http://dx.doi.org/10.1093/bioinformatics/bts606). Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance data format for WGS variant calls. *Bioinformatics*. [DOI: 10.1093/bioinformatics/btx145](http://dx.doi.org/10.1093/bioinformatics/btx145). ## Package Maintainer Dr. Xiuwen Zheng ([zhengxwen@gmail.com](zhengxwen@gmail.com)) ## URL [http://github.com/zhengxwen/gdsfmt](http://github.com/zhengxwen/gdsfmt) [http://www.bioconductor.org/packages/gdsfmt](http://www.bioconductor.org/packages/gdsfmt) ## Installation * Bioconductor repository: ```R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("gdsfmt") ``` * Development version from Github (for developers/testers only): ```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, 2007-2020, Xiuwen Zheng * zlib, zlib License, 1995-2017, Jean-loup Gailly and Mark Adler * LZ4, BSD 2-clause License, 2011-2019, Yann Collet * liblzma, public domain, 2005-2018, Lasse Collin and other xz contributors * [README](./inst/COPYRIGHTS) ## GDS Command-line Tools In the R environment, ```R install.packages("getopt", repos="http://cran.r-project.org") install.packages("optparse", repos="http://cran.r-project.org") install.packages("crayon", repos="http://cran.r-project.org") if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("gdsfmt") ``` [See More...](https://github.com/zhengxwen/Documents/tree/master/Program) ### *viewgds* `viewgds` is a shell script written in R ([viewgds.R](https://github.com/zhengxwen/Documents/blob/master/Program/viewgds.R)), to view the contents of a GDS file. The R packages `gdsfmt`, `getopt` and `optparse` should be installed before running `viewgds`, and the package `crayon` is optional. ``` Usage: viewgds [options] file ``` Installation with command line, ```sh curl -L https://raw.githubusercontent.com/zhengxwen/Documents/master/Program/viewgds.R > viewgds chmod +x viewgds ## Or wget -qO- --no-check-certificate https://raw.githubusercontent.com/zhengxwen/Documents/master/Program/viewgds.R > viewgds chmod +x viewgds ``` ### *diffgds* `diffgds` is a shell script written in R ([diffgds.R](https://github.com/zhengxwen/Documents/blob/master/Program/diffgds.R)), to compare two files GDS files. The R packages `gdsfmt`, `getopt` and `optparse` should be installed before running `diffgds`. ``` Usage: diffgds [options] file1 file2 ``` Installation with command line, ```sh curl -L https://raw.githubusercontent.com/zhengxwen/Documents/master/Program/diffgds.R > diffgds chmod +x diffgds ## Or wget -qO- --no-check-certificate https://raw.githubusercontent.com/zhengxwen/Documents/master/Program/diffgds.R > diffgds chmod +x diffgds ``` ## Examples ```R library(gdsfmt) # create a GDS file f <- createfn.gds("test.gds") add.gdsn(f, "int", val=1:10000) add.gdsn(f, "double", val=seq(1, 1000, 0.4)) add.gdsn(f, "character", val=c("int", "double", "logical", "factor")) add.gdsn(f, "logical", val=rep(c(TRUE, FALSE, NA), 50)) add.gdsn(f, "factor", val=as.factor(c(NA, "AA", "CC"))) add.gdsn(f, "bit2", val=sample(0:3, 1000, replace=TRUE), storage="bit2") # list and data.frame add.gdsn(f, "list", val=list(X=1:10, Y=seq(1, 10, 0.25))) add.gdsn(f, "data.frame", val=data.frame(X=1:19, Y=seq(1, 10, 0.5))) folder <- addfolder.gdsn(f, "folder") add.gdsn(folder, "int", val=1:1000) add.gdsn(folder, "double", val=seq(1, 100, 0.4)) # show the contents f # close the GDS file closefn.gds(f) ``` ``` File: test.gds (1.1K) + [ ] |--+ int { Int32 10000, 39.1K } |--+ double { Float64 2498, 19.5K } |--+ character { Str8 4, 26B } |--+ logical { Int32,logical 150, 600B } * |--+ factor { Int32,factor 3, 12B } * |--+ bit2 { Bit2 1000, 250B } |--+ list [ list ] * | |--+ X { Int32 10, 40B } | \--+ Y { Float64 37, 296B } |--+ data.frame [ data.frame ] * | |--+ X { Int32 19, 76B } | \--+ Y { Float64 19, 152B } \--+ folder [ ] |--+ int { Int32 1000, 3.9K } \--+ double { Float64 248, 1.9K } ``` ## Also See [pygds](https://github.com/CoreArray/pygds): Python interface to CoreArray Genomic Data Structure (GDS) files [jugds.jl](https://github.com/CoreArray/jugds.jl): Julia interface to CoreArray Genomic Data Structure (GDS) files