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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.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 |