BSraw-class             Class to contain raw Bisulfite Sequencing
                        (BiSeq) Data
BSrel-class             Class to contain Bisulfite Sequencing (BiSeq)
                        Data
DMRs                    The output of 'findDMRs'
annotateGRanges         Annotates a 'GRanges' object by means of a
                        second 'GRanges' object
betaRegression          A function to estimate and test a group factor
                        within a beta regression
betaResults             The output of 'betaRegression'
betaResultsNull         The output of 'betaRegression' for resampled
                        data
binomLikelihoodSmooth   Calculates local likelihood estimations for
                        binomial random variables
clusterSites            Assigns CpG cluster memberships on CpG sites
                        within 'BSraw' objects
clusterSitesToGR        A function to obtain a 'GRanges' object of CpG
                        clusters from 'BSraw' and 'BSrel' objects
compareTwoSamples       Detects DMRs by comparing two samples
covBoxplots             Creates boxplots of coverages per sample
covStatistics           Prints a short summary of coverage statistics
                        per sample
estLocCor               Estimates the correlations of the z-scores
filterByCov             Filters regions (or single CpGs) of a 'BSraw'
                        object with a minimum coverage
filterBySharedRegions   Reduces a 'BSraw' or 'BSrel' object to regions
                        (or single CpGs) shared by a fraction of
                        samples
findDMRs                Aggregates CpG sites to DMRs
globalTest              Test whether at least one CpG is differentially
                        methylated in a given genomic region
limitCov                Limits the coverage of a 'BSraw' object
logisticRegression      Estimates and tests a group factor
makeVariogram           Variogram estimator.
plotBindingSites        Plots the mean methylation of given regions
plotMeth                Plots raw and smoothed methylation data for a
                        given region
plotMethMap             Plots methylation values of multiple samples in
                        a given region
plotSmoothMeth          Plots smoothed methylation values for a bunch
                        of samples and a given region
predictMeth             Predicts methylation levels along CpG sites or
                        for a grid of sites in CpG clusters.
predictedMeth           The output of 'predictMeth'
promoters               A 'GRanges' of promoters of the human genome
rawToRel                Converts a 'BSraw' object to a 'BSrel' object
readBismark             Reads cytosine methylation stati determined by
                        Bismark
rrbs                    RRBS data of APL patient samples and controls.
smoothVariogram         Smoothes variogram
summarizeRegions        Aggregates methylation information of single
                        CpG sites
testClusters            Tests CpG clusters
trimClusters            Trims CpG clusters
vario                   Output of 'makeVariogram'
writeBED                Writes 'BSraw' and 'BSrel' data to a bed file
                        suitable for the IGV
