gdsfmt
R Interface to CoreArray Genomic Data Structure (GDS) Files
Bioconductor version: Release (3.20)
Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is 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 [ctb] (for the included liblzma sources)
Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>
citation("gdsfmt")):
Installation
To install this package, start R (version "4.4") 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 | 1.42.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 years) |
| License | LGPL-3 |
| Depends | R (>= 2.15.0), methods |
| Imports | |
| System Requirements | |
| URL | https://github.com/zhengxwen/gdsfmt |
| Bug Reports | https://github.com/zhengxwen/gdsfmt/issues |
See More
| Suggests | parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | bigmelon, GDSArray, RAIDS, SAIGEgds, SCArray, SeqArray, SNPRelate, Mega2R |
| Imports Me | CNVRanger, GBScleanR, GENESIS, ggmanh, GWASTools, SCArray.sat, SeqSQC, SeqVarTools, VariantExperiment, EthSEQ, gwid, simplePHENOTYPES, snplinkage |
| 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_1.42.0.tar.gz |
| Windows Binary (x86_64) | gdsfmt_1.42.0.zip |
| macOS Binary (x86_64) | gdsfmt_1.42.0.tgz |
| macOS Binary (arm64) | gdsfmt_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gdsfmt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gdsfmt |
| Bioc Package Browser | https://code.bioconductor.org/browse/gdsfmt/ |
| Package Short Url | https://bioconductor.org/packages/gdsfmt/ |
| Package Downloads Report | Download Stats |