To install this package, start R and enter:

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

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

VegaMC

 

VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

Bioconductor version: Release (3.1)

This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

Author: S. Morganella and M. Ceccarelli

Maintainer: Sandro Morganella <sandro at ebi.ac.uk>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("VegaMC")

 

PDF R Script VegaMC
PDF   Reference Manual

Details

biocViews CopyNumberVariation, Software, aCGH
Version 3.6.0
In Bioconductor since BioC 2.10 (R-2.15) (3.5 years)
License GPL-2
Depends R (>= 2.10.0), biomaRt, Biobase, genoset
Imports methods
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source VegaMC_3.6.0.tar.gz
Windows Binary VegaMC_3.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VegaMC_3.6.0.tgz
Mac OS X 10.9 (Mavericks) VegaMC_3.6.0.tgz
Subversion source (username/password: readonly)
GitHub source https://github.com/Bioconductor-mirror/VegaMC/tree/release-3.1
Package Short Url http://bioconductor.org/packages/VegaMC/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center