gdsfmt
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see gdsfmt.
R Interface to CoreArray Genomic Data Structure (GDS) Files
Bioconductor version: 3.9
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.
Author: Xiuwen 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)
Maintainer: Xiuwen Zheng <zhengxwen at gmail.com>
citation("gdsfmt")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gdsfmt")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gdsfmt")| Introduction to GDS Format | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | LGPL-3 |
| Depends | R (>= 2.15.0), methods |
| Imports | |
| System Requirements | |
| URL | http://corearray.sourceforge.net/ http://github.com/zhengxwen/gdsfmt |
| Bug Reports | http://github.com/zhengxwen/gdsfmt/issues |
See More
| Suggests | parallel, digest, crayon, RUnit, knitr, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | bigmelon, GDSArray, SeqArray, SNPRelate |
| Imports Me | CNVRanger, GENESIS, GWASTools, SeqSQC, SeqVarTools |
| Suggests Me | AnnotationHub, HIBAG |
| Links To Me | SeqArray, SNPRelate |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gdsfmt_1.20.0.tar.gz |
| Windows Binary | gdsfmt_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | gdsfmt_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gdsfmt |
| Source Repository (Developer Access) | git clone [email protected]:packages/gdsfmt |
| Bioc Package Browser | https://code.bioconductor.org/browse/gdsfmt/ |
| Package Short Url | https://bioconductor.org/packages/gdsfmt/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |