Block.GUI               Generate interactive plot for the result of
                        champ.Block() function,
ChAMP-package           ChAMP-Chip Analysis Methylation Pipeline
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
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.GSEA              Do GSEA for DMP, DMR and other methylation data
                        related results.
champ.QC                Plot quality control plot, mdsplot,
                        densityPlot, dendrogram for a data set.
champ.SVD               Singular Value Decomposition analysis for batch
                        effects prediciton in HumanMethylation450 or
                        HumanMethylationEPIC data
champ.ebGSEA            Empirical Bayes GSEA method.
champ.filter            Do filtering on beta, M, intensity, Meth and
                        UnMeth matrix.
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.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.
