To install this package, start R and enter:

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

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

ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: Release (2.14)

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

Author: Tiffany Morris, Lee Butcher, Andy Feber, Andrew Teschendorff, Ankur Chakravarthy and Stephan Beck

Maintainer: Tiffany Morris <Tiffany.Morris at ucl.ac.uk>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("ChAMP")

 

PDF R Script Package
PDF   Reference Manual

Details

biocViews CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 1.2.8
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-3
Depends R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db
Imports sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source ChAMP_1.2.8.tar.gz
Windows Binary ChAMP_1.2.8.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChAMP_1.2.8.tgz
Mac OS X 10.9 (Mavericks) ChAMP_1.2.8.tgz
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