RUVadj                  RUV adjust
RUVfit                  Remove unwanted variation when testing for
                        differential methylation
SWAN                    Subset-quantile Within Array Normalisation for
                        Illumina Infinium HumanMethylation450 BeadChips
contrasts.varFit        Compute contrasts for a varFit object.
densityByProbeType      Plot the beta value distributions of the
                        Infinium I and II probe types relative to the
                        overall beta value distribution.
getAdj                  Extract values adjusted for unwanted variation
                        by RUVm
getINCs                 Extract intensity data for Illumina negative
                        controls found on 450k or EPIC arrays.
getLeveneResiduals      Obtain Levene residuals
getMappedEntrezIDs      Get mapped Entrez Gene IDs from CpG probe names
gometh                  Gene ontology testing for Ilumina methylation
                        array data
goregion                Gene ontology testing of DMRs for Ilumina
                        methylation array data
gsameth                 Generalised gene set testing for Illumina's
                        methylation array data
gsaregion               Generalised gene set testing for Illumina's
                        methylation array data
gsaseq                  Generalised gene set testing for RNA-seq data
missMethyl-package      Introduction to the missMethyl package
topGSA                  Get table of top 20 enriched pathways
topRUV                  Table of top-ranked differentially methylated
                        CpGs obatained from a differential methylation
                        analysis using RUV
topVar                  Table of top-ranked differentially variable
                        CpGs
varFit                  Testing for differential variability
