source("http://bioconductor.org/biocLite.R")
biocLite("genoset")

genoset

Provides classes similar to ExpressionSet for copy number analysis

Bioconductor version: 2.13

Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

Author: Peter M. Haverty

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

Installation

To install this package, start R and enter:

source("http://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	CopyNumberVariants, DataRepresentation, Infrastructure, Microarray, SNP, Software
Version	1.14.0
In Bioconductor since	BioC 2.8 (R-2.13)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics(>= 0.1.6), Biobase(>= 2.15.1), IRanges, GenomicRanges
Imports	methods, graphics, IRanges, GenomicRanges
Suggests	RUnit, DNAcopy, stats, BSgenome, Biostrings
System Requirements
URL
Depends On Me	VegaMC
Imports Me	methyAnalysis
Suggests Me

Package Archives

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

Package Source	genoset_1.14.0.tar.gz
Windows Binary	genoset_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	genoset_1.14.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats