gdsfmt
This is the released version of gdsfmt; for the devel version, see gdsfmt.
R Interface to CoreArray Genomic Data Structure (GDS) Files
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.48.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 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
Follow Installation instructions to use this package in your R session.
| Source Package | gdsfmt_1.48.2.tar.gz |
| Windows Binary (x86_64) | gdsfmt_1.48.2.zip |
| macOS Binary (big-sur-x86_64) | gdsfmt_1.48.2.tgz |
| macOS Binary (sonoma-arm64) | gdsfmt_1.48.2.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 |
| Old Source Packages for BioC 3.23 | Source Archive |