Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Documentation for package ‘ChAMP’ version 2.39.1

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.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