RAdat                   A simulated methylation dataset based on a real
                        data.
RAdat2                  A simulated methylation dataset based on a real
                        data.
binomRegMethModel       A smoothed-EM algorithm to estimate covariate
                        effects and test regional association in
                        Bisulfite Sequencing-derived methylation data
binomRegMethModelPlot   Plot the smooth covariate effect
binomRegMethModelPred   A smoothed-EM algorithm to estimate covariate
                        effects and test regional association in
                        Bisulfite Sequencing-derived methylation data
binomRegMethModelSim    Simulate Bisulfite sequencing data from
                        specified smooth covariate effects
binomRegMethPredPlot    Plot the predicted methylation levels
formatFromBSseq         Parsing output from the BSseq package
formatFromBismark       Parsing output from the Bismark alignment suite
runSOMNiBUS             Wrapper function running the smoothed-EM
                        algorithm to estimate covariate effects and
                        test regional association in Bisulfite
                        Sequencing-derived methylation data
splitDataByBed          Split methylation data into regions based on
                        the genomic annotations
splitDataByChromatin    Split methylation data into regions based on
                        the chromatin states
splitDataByDensity      Split methylation data into regions based on
                        the density of CpGs
splitDataByGRanges      Split methylation data into regions based on
                        the genomic annotations
splitDataByGene         Split methylation data into regions based on
                        the genes annotations
splitDataByRegion       Split methylation data into regions based on
                        the spacing of CpGs
