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ChAMP (version 1.10.0)

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Description

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations. In addition there is a method to help calculate hmC using BS and oxBS samples.

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Version

Version

1.10.0

License

GPL-3

Maintainer

Yuan Tian Tiffany Morris

Last Published

February 15th, 2017

Functions in ChAMP (1.10.0)

champ.TrueMethyl

Identify Most Variable Positions between oxBS TrueMethyl Samples and BS samples in Illumina HumanMethylation450 data.
ChAMP-package

ChAMP-Chip Analysis Methylation Pipeline
champ.DMR

Applying Bumphunter or ProbeLasso Algorithms to detect Different Methylation Regions in a beta valued Methylation Dataset.
champ.norm

Normalization of HumanMethylation450 data
champ.SVD

Singular Value Decomposition analysis for batch effects prediciton in HumanMethylation450 data
champ.load

Upload of raw HumanMethylation450 data from IDAT files.
champ.CNA

Inference of Copy Number Abberrations from intensity values.
champ.runCombat

Function that uses ComBat to correct for batch effects related to slide/BeadChip.
champ.refbase

Applying References-Base Methold to beta valued methylation data.
champ.process

Process function to run all methods in ChAMP pipeline.
champ.MVP

Identify Most Variable Positions in Illumina HumanMethylation450 data.
champ.reffree

Applying RefFreeEWAS Methold to beta valued methylation data.