DMRcaller               Call Differentially Methylated Regions (DMRs)
                        between two samples
DMRsNoiseFilterCG       The DMRs between WT and met1-3 in CG context
GEs                     The genetic elements data
analyseReadsInsideRegionsForCondition
                        Analyse reads inside regions for condition
computeDMRs             Compute DMRs
computeDMRsReplicates   Compute DMRs
computeMethylationDataCoverage
                        Compute methylation data coverage
computeMethylationDataSpatialCorrelation
                        Compute methylation data spatial correlation
computeMethylationProfile
                        Compute methylation profile
computeOverlapProfile   Compute Overlaps Profile
extractGC               Extract GC
filterDMRs              Filter DMRs
getWholeChromosomes     Get whole chromosomes from methylation data
joinReplicates          Joins together two GRange objects in a single
                        containing all the replicates
mergeDMRsIteratively    Merge DMRs iteratively
methylationDataList     The methylation data list
plotLocalMethylationProfile
                        Plot local methylation profile
plotMethylationDataCoverage
                        Plot methylation data coverage
plotMethylationDataSpatialCorrelation
                        Plot methylation data spatial correlation
plotMethylationProfile
                        Plot Methylation Profile
plotMethylationProfileFromData
                        Plot methylation profile from data
plotOverlapProfile      Plot overlap profile
poolMethylationDatasets
                        Pool methylation data
poolTwoMethylationDatasets
                        Pool two methylation datasets
readBismark             Read Bismark
readBismarkPool         Read Bismark pool
saveBismark             Save Bismark
syntheticDataReplicates
                        Simulated data for biological replicates
