Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

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Documentation for package ‘ChAMP’ version 2.38.0

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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.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