# Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

## Documentation for package ‘ChAMP’ version 2.16.0

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

## Help Pages

ChAMP-package | ChAMP-Chip Analysis Methylation Pipeline
Block.GUI | Generate interactive plot for the result of champ.Block() function,
ChAMP | ChAMP-Chip Analysis Methylation Pipeline
champ.Block | Identify Differential Methylation Blocks in Illumina HumanMethylation450 or HumanMethylationEPIC data.
champ.CNA | Inference of Copy Number Abberrations from intensity values.
champ.DMP | Identify Differential Methylation Positions (DMP) and Numeric Covariate related CpGs in Illumina HumanMethylation450 or HumanMethylationEPIC data.
champ.DMR | Applying Bumphunter, DMRcate or ProbeLasso Algorithms to detect Different Methylation Regions in a beta valued Methylation Dataset.
champ.ebGSEA | Empirical Bayes GSEA method.
champ.EpiMod | champ.EpiMod() infer differential methylation interactome hotspots.
champ.filter | Do filtering on beta, M, intensity, Meth and UnMeth matrix.
champ.GSEA | Do GSEA for DMP, DMR and other methylation data related results.
champ.import | Read data from IDAT file.
champ.impute | Conduct imputation for NA value on beta matrix and corresponding pd(Sample_sheet.csv) file.
champ.load | Upload of raw HumanMethylation450K or HumanMethylationEPIC data from IDAT files.
champ.norm | Normalization for HumanMethylation450 or HumanMethylationEPIC data
champ.process | Process function to run all methods in ChAMP pipeline.
champ.QC | Plot quality control plot, mdsplot, densityPlot, dendrogram for a data set.
champ.refbase | Applying References-Base Methold to beta valued methylation data.
champ.runCombat | Function that uses ComBat to correct for batch effects. Multiple batch effect correction is allowed.
champ.SVD | Singular Value Decomposition analysis for batch effects prediciton in HumanMethylation450 or HumanMethylationEPIC data
CpG.GUI | Generate interactive plot for summary information of a list of CpGs
DMP.GUI | Generate interactive plot for the result of champ.DMP() function,
DMR.GUI | Generate interactive plot for the result of champ.DMR() function,
QC.GUI | Generate interactive plot for Quality Control of a dataset