gdsfmt
R Interface to CoreArray Genomic Data Structure (GDS) Files
Bioconductor version: 3.23 · Package version: 1.48.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gdsfmt")Details
| Maintainer | Xiuwen Zheng <zhengx@u.washington.edu> |
| Author | Xiuwen Zheng [aut, cre] (<https://orcid.org/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) |
| License | LGPL-3 |
| URL | https://github.com/zhengxwen/gdsfmt |
| Bug Reports | https://github.com/zhengxwen/gdsfmt/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/gdsfmt/ |
Citation
From within R, enter citation("gdsfmt"):
Xiuwen Zheng. gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files. doi:10.18129/B9.bioc.gdsfmt, R package version 1.48.2, https://bioconductor.org/packages/gdsfmt.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | gdsfmt_1.48.2.tgz |
| macOS binary (x86_64) | gdsfmt_1.48.2.tgz |
Dependencies
Depends: R (>= 2.15.0), methods
Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics
Reverse dependencies
Depends On Me (7): bigmelon, GDSArray, RAIDS, SAIGEgds, SCArray, SeqArray, SNPRelate
Imports Me (14): CNVRanger, CoxMK, EthSEQ, GBScleanR, GENESIS, ggmanh, GWASTools, gwid, SCArray.sat, SeqSQC, SeqVarTools, simplePHENOTYPES, snplinkage, VariantExperiment
Suggests Me (2): AnnotationHub, HIBAG