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GDSArray

This is the development version of GDSArray; for the stable release version, see GDSArray.

Representing GDS files as array-like objects

Bioconductor version: Development (3.18)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataRepresentation, GenotypingArray, Infrastructure, Sequencing, Software
Version 1.21.0
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
Linking To
Suggests testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
System Requirements
Enhances
URL https://github.com/Bioconductor/GDSArray
Bug Reports https://github.com/Bioconductor/GDSArray/issues
See More
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_1.21.0.tar.gz
Windows Binary GDSArray_1.21.0.zip (64-bit only)
macOS Binary (x86_64) GDSArray_1.21.0.tgz
macOS Binary (arm64)
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