To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

genoset

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see genoset.

Provides classes similar to ExpressionSet for copy number analysis

Bioconductor version: 3.0

Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a GRanges object. This object contains feature genome location data and provides for efficient subsetting on genome location. Provides convenience functions for processing of copy number and B-Allele Frequency data. Provides the class RleDataFrame to store runs of data along the genome for multiple samples.

Author: Peter M. Haverty

Maintainer: Peter M. Haverty <phaverty at gene.com>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("genoset")
PDF R Script genoset
PDF Reference Manual
Text NEWS

Details

biocViews CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version 1.20.0
In Bioconductor since BioC 2.8 (R-2.13) (5 years)
License Artistic-2.0
Depends R (>= 2.10), BiocGenerics(>= 0.11.3), Biobase(>= 2.15.1), GenomicRanges(>= 1.17.19)
Imports S4Vectors(>= 0.2.3), GenomeInfoDb(>= 1.1.3), IRanges, methods, graphics
LinkingTo
Suggests RUnit, DNAcopy, stats, BSgenome, Biostrings
SystemRequirements
Enhances parallel
URL https://github.com/phaverty/genoset
Depends On Me VegaMC
Imports Me methyAnalysis
Suggests Me
Build Report

Package Archives

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

Package Source genoset_1.20.0.tar.gz
Windows Binary genoset_1.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) genoset_1.20.0.tgz
Mac OS X 10.9 (Mavericks) genoset_1.20.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/genoset/tree/release-3.0
Package Short Url http://bioconductor.org/packages/genoset/
Package Downloads Report Download Stats

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