ChAMP (version 1.10.0)

ChAMP-package: ChAMP-Chip Analysis Methylation Pipeline

Description

A pipeline that enables pre-processing of 450k data, a selection of normalization methods and novel methods for downstream analysis including Probe Lasso DMR Hunter and Copy Number Alteration analysis.

Details

Package:

ChAMP

Type:

Package

Version:

1.9.2

Date:

2016-03-13

License:

GPL-3

The full analysis pipeline can be run with all defaults using champ.process()

Alternatively, it can be run in steps using all functions separately.

Examples

	directory=system.file('extdata',package='ChAMPdata')
	champ.process(directory=directory)
	myLoad=champ.load()
	myNorm=champ.norm()
    myRefBase=champ.refbase()
	champ.SVD()
	batchNorm=champ.runCombat()
	limma=champ.MVP()
	myDMR=champ.DMR()
	champ.CNA()