GDSArray

This is the released version of GDSArray; for the devel version, see GDSArray.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Representing GDS files as array-like objects

Bioconductor version: Release (3.23)

GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.

Author: Qian Liu [aut], Martin Morgan [aut], Hervé Pagès [aut], Xiuwen Zheng [aut, cre]

Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>

Citation (from within R, enter citation("GDSArray")):

Qian Liu, Martin Morgan, Hervé Pagès, Xiuwen Zheng. GDSArray: Representing GDS files as array-like objects. doi:10.18129/B9.bioc.GDSArray, R package version 1.32.0, https://bioconductor.org/packages/GDSArray.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GDSArray")

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("GDSArray")

GDSArray: Representing GDS files as array-like objects	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, GenotypingArray, Infrastructure, Sequencing, Software
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	GPL-3
Depends	R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32)
Imports	tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
System Requirements
URL	https://github.com/Bioconductor/GDSArray
Bug Reports	https://github.com/Bioconductor/GDSArray/issues

Suggests	testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
Linking To
Enhances
Depends On Me
Imports Me	CNVRanger, VariantExperiment
Suggests Me	DelayedDataFrame
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GDSArray_1.32.0.tar.gz
Windows Binary (x86_64)	GDSArray_1.32.0.zip
macOS Binary (big-sur-x86_64)	GDSArray_1.32.0.tgz
macOS Binary (sonoma-arm64)	GDSArray_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GDSArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GDSArray
Package Short Url	https://bioconductor.org/packages/GDSArray/
Package Downloads Report	Download Stats