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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.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 |