gdsfmt
This is thereleased version of gdsfmt; for the devel version, seegdsfmt.
R Interface to CoreArray Genomic Data Structure (GDS) Files
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0002-1390-0708, 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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("gdsfmt")For older versions of R, please refer to the appropriateBioconductor 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 | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (11 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 |
| Imports Me | CNVRanger,GBScleanR,GENESIS,ggmanh,GWASTools,SCArray.sat,SeqSQC,SeqVarTools,VariantExperiment,CoxMK,EthSEQ,gwid,simplePHENOTYPES,snplinkage |
| Suggests Me | AnnotationHub,HIBAG |
| Links To Me | SeqArray,SNPRelate |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | gdsfmt_1.46.0.tar.gz |
| Windows Binary (x86_64) | gdsfmt_1.46.0.zip |
| macOS Binary (x86_64) | gdsfmt_1.46.0.tgz |
| macOS Binary (arm64) | gdsfmt_1.46.0.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 |