# Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

## Documentation for package ‘ChAMP’ version 1.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ChAMP-package | ChAMP-Chip Analysis Methylation Pipeline
ChAMP | ChAMP-Chip Analysis Methylation Pipeline
champ.CNA | Inference of Copy Number Abberrations from intensity values.
champ.lasso | Probe Lasso DMR Hunter
champ.load | Upload of raw HumanMethylation450 data from IDAT files.
champ.MVP | Identify Most Variable Positions in Illumina HumanMethylation450 data.
champ.norm | Normalization of HumanMethylation450 data
champ.process | Process function to run all methods in ChAMP pipeline.
champ.runCombat | Function that uses ComBat to correct for batch effects related to slide/BeadChip.
champ.SVD | Singular Value Decomposition analysis for batch effects prediciton in HumanMethylation450 data
champ.TrueMethyl | Identify Most Variable Positions between oxBS TrueMethyl Samples and BS samples in Illumina HumanMethylation450 data.