GDSArray

DOI: 10.18129/B9.bioc.GDSArray  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GDSArray.

Representing GDS files as array-like objects

Bioconductor version: 3.17

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, cre], Martin Morgan [aut], Hervé Pagès [aut], Xiuwen Zheng [aut]

Maintainer: Qian Liu <qliu7 at buffalo.edu>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	DataRepresentation, GenotypingArray, Infrastructure, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 years)
License	GPL-3
Depends	R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray(>= 0.5.32)
Imports	tools, S4Vectors(>= 0.17.34), SNPRelate, SeqArray
LinkingTo
Suggests	testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
SystemRequirements
Enhances
URL	https://github.com/Bioconductor/GDSArray
BugReports	https://github.com/Bioconductor/GDSArray/issues
Depends On Me
Imports Me	CNVRanger, VariantExperiment
Suggests Me	DelayedDataFrame
Links To Me
Build Report

Package Archives

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

Source Package	GDSArray_1.20.0.tar.gz
Windows Binary	GDSArray_1.20.0.zip
macOS Binary (x86_64)	GDSArray_1.20.0.tgz
macOS Binary (arm64)	GDSArray_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GDSArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GDSArray
Bioc Package Browser	https://code.bioconductor.org/browse/GDSArray/
Package Short Url	https://bioconductor.org/packages/GDSArray/
Package Downloads Report	Download Stats