MethyGenoSet-class      Class MethyGenoSet: contain and describe
                        Illumina Infinium methylation data in
                        GenoSet-class
MethyLumiM2GenoSet      Coerce objects of MethyLumiM-class to
                        MethyGenoSet
annotateDMRInfo         Annotate the DMR (Differentially Methylated
                        Region)
annotateGRanges         Annotate a GRanges object
asBigMatrix-methods     convert the data matrix in the assayData of a
                        GenoSet as BigMatrix
buildAnnotationTracks   Build annotation tracks for visualizing using
                        Gviz package
checkChrName            check chromosome names
createTranscriptTrack   Create a transcript annotation track
detectDMR.slideWin      Detect DMR (Differentially Methylated Region)
                        using slide window smoothing
estimateCMR.methylation
                        Estimate the averaged methylation levels within
                        a chromosome region or transcript promoter
estimateMethySeq        Estimate the methylation level (Beta-value) of
                        Methyl-Seq data
exampleMethyGenoSet     Example MethyGenoSet dataset
export.DMRInfo          Output the DMR (Differentially Methylated
                        Region) data information
export.methyGenoSet     Export a MethyGenoSet object to be visualized
                        using external genome browser tools
filterBisulfiteVariant
                        filtering the variant calls of Bisulfite
                        converted sequencing data
getContinuousRegion     Get continuous chromosome region by merging
                        nearby or overlapping regions
getCoverage             get the coverage based on a given GRanges
                        object
heatmapByChromosome     heatmap with chromosome location as x axis
identifyCpG             Identify the CpG-site locations from a genome
                        library
identifySigDMR          Identify significantly DMR (Differentially
                        Methylated Region)
plotHeatmapByGene       plot methylation heatmap by genes
plotMethylationHeatmapByGene
                        plot methylation heatmap by genes
plotTracksWithDataTrackInfo
                        plot Tracks with additional DataTrack
                        information added to the left of the plot
smoothMethyData         Smooth the methylation data
updateMethyGenoSet      Update old version MethyGenoSet objects
