GDSArray

DOI: 10.18129/B9.bioc.GDSArray    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GDSArray.

Representing GDS files as array-like objects

Bioconductor version: 3.7

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 [ctb], Hervé Pagès [ctb]

Maintainer: Qian Liu <Qian.Liu at roswellpark.org>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GDSArray")

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	Annotation, Coverage, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software, VariantAnnotation
Version	1.0.0
License	GPL-3
Depends	R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray(>= 0.5.32)
Imports	tools, S4Vectors(>= 0.17.43), IRanges, SNPRelate, SeqArray
LinkingTo
Suggests	testthat, knitr, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/Bioconductor/GDSArray
BugReports	https://github.com/Bioconductor/GDSArray/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GDSArray_1.0.0.tar.gz
Windows Binary	GDSArray_1.0.0.zip
Mac OS X 10.11 (El Capitan)	GDSArray_1.0.0.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	http://bioconductor.org/packages/GDSArray/
Package Downloads Report	Download Stats