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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 (3.19)

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 "4.4") 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

Reference Manual PDF

Details

biocViews DataRepresentation, GenotypingArray, Infrastructure, Sequencing, Software
Version 1.23.3
In Bioconductor since BioC 3.7 (R-3.5) (6 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
See More
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

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/GDSArray/
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