Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC


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Documentation for package ‘ChAMP’ version 1.10.0

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ChAMP-package ChAMP-Chip Analysis Methylation Pipeline
ChAMP ChAMP-Chip Analysis Methylation Pipeline
champ.CNA Inference of Copy Number Abberrations from intensity values.
champ.DMR Applying Bumphunter or ProbeLasso Algorithms to detect Different Methylation Regions in a beta valued Methylation Dataset.
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.refbase Applying References-Base Methold to beta valued methylation data.
champ.reffree Applying RefFreeEWAS Methold to beta valued methylation data.
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.