.analyseReadsInsideBins
                        Analyse reads inside regions
.analyseReadsInsideBinsOneSample
                        Analyse reads inside regions for one sample
.analyseReadsInsideBinsPMDs
                        Analyse reads inside regions
.analyseReadsInsideBinsReplicates
                        Analyse reads inside regions
.analyseReadsInsideRegions
                        Analyse reads inside regions
.analyseReadsInsideRegionsForCondition
                        Analyse reads inside regions
.analyseReadsInsideRegionsOneSample
                        Analyse reads inside regions
.analyseReadsInsideRegionsPMDs
                        Analyse reads inside regions
.analyseReadsInsideRegionsReplicates
                        Analyse reads inside regions
.analyseReadsInsideRegionsVMDs
                        Analyse reads inside regions with computing
                        mean and standard deviation per-read
                        proportions
.analyseReadsInsideRegionsVMR
                        Analyse reads inside regions (with VMR testing)
.computeaAjustedPValuesInDMRs
                        Compute adjusted p-values in DMRs
.computeaAjustedPValuesInDMRsReplicates
                        Compute adjusted p-values
.computeAdjuestedPValues
                        Compute adjusted p-values
.computeAdjuestedPValuesReplicates
                        Compute adjusted p-values
.computeBetaReg         This function applies the .computeBetaRegSingle
                        to the entire dataset
.computeBetaRegSingle   Beta regression
.computeDMRsBins        This function computes the differentially
                        methylated regions between two conditions using
                        the bins method.
.computeDMRsNeighbourhood
                        This function computes the differentially
                        methylated regions between two conditions using
                        the neighbourhood method. This assumes the
                        computation of differentially methylated
                        cytosines followed by smart merging of these
                        cytosines while keeping the new DMRs
                        statistically significant.
.computeDMRsNoiseFilter
                        This function computes the differentially
                        methylated regions between two conditions using
                        the noise filter method.
.computeDMRsReplicatesBins
                        This function computes the differentially
                        methylated regions between replicates using the
                        bins method.
.computeDMRsReplicatesNeighbourhood
                        This function computes the differentially
                        methylated regions between replicates using the
                        neighbourhood method.
.computeMethylationDataSpatialCorrelation
                        Compute methylation data spatial correlation
.computePMDsBins        This function computes the partially methylated
                        regions using the bins method.
.computePMDsNeighbourhood
                        This function computes the partially methylated
                        domains using the neighbourhood method. This
                        assumes the computation of partially methylated
                        cytosines followed by smart merging of these
                        cytosines while keeping the new PMDs
                        statistically significant.
.computePMDsNoiseFilter
                        This function computes the partially methylated
                        regions using the noise filter method.
.computeProportionsInDMRs
                        This function recalculate proportions between
                        methylated and total reads in a new region.
.computeVMDsBins        This function computes the variance methylated
                        regions using the bins method.
.convertResult          This function extracts the p-value for each
                        cytosine from the betareg object
.countCytosinesInside   Count cytosines inside
.countMethylationDataCoverage
                        Count methylation data coverage
.countTotalNumberOfCytosines
                        Count total number of Cytosines
.fisherTest             Fisher test
.fisherTestPValue       Fisher test
.isColor                Is color
.isInteger              .is.integer
.joinMethylationData    Join methylation data
.mergeDMRsIteratively   This takes a list of DMRs and attempts to merge
                        DMRs while keeping the new DMRs statistically
                        significant
.mergePMDsIteratively   This takes a list of PMDs and attempts to merge
                        PMDs while keeping the new PMDs filtering by
                        the preset parameter
.movingAverage          Moving average
.movingSum              Moving sum
.plotGeneticElements    Plot genetic elements
.printGenomicRanges     Print GenomicRanges
.scoreTest              Score test
.smartMergeDMRs         This takes a list of DMRs and attempts to merge
                        DMRs while keeping the new DMRs statistically
                        significant
.smartMergeDMRsReplicates
                        This takes a list of DMRs and attempts to merge
                        DMRs while keeping the new DMRs statistically
                        significant
.smartMergePMDs         This takes a list of PMDs and attempts to merge
                        PMDs while keeping the new PMDs statistically
                        significant
.splitGRangesEqualy     .splitGRangesEqualy
.stopIfNotAll           .stopIfNotAll
.validateConditionReplicates
                        Validate the condition of the experiment
.validateGRanges        Validate GRanges
.validateMethylationData
                        Validate methylation data
.validateMethylationDataList
                        Validate methylation data
.validateMethylationProfile
                        Validate methylation profile
.validateModif          Validate Modification Tag in BAM
.validateStatisticalTest
                        Validate statistial test
.validateStatisticalTestReplicates
                        Validate statistial test
analyseReadsInsideRegionsForCondition
                        Analyse reads inside regions for condition
analyseReadsInsideRegionsForConditionPMD
                        Analyse reads inside regions for condition
computeCoMethylatedPositions
                        Compute pairwise co-methylation statistics for
                        cytosine sites within regions
computeCoMethylatedRegions
                        Compute pairwise co-methylation statistics
                        between regions
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
computePMDs             Compute PMDs
computeVMDs             Compute VMDs
DMRcaller               Call Differentially Methylated Regions (DMRs)
                        between two samples
DMRsNoiseFilterCG       The DMRs between WT and met1-3 in CG context
extractGC               Extract GC
filterDMRs              Filter DMRs
filterPMDs              Filter PMDs
filterVMDs              Filter VMDs
filterVMRsONT           Filter VMRs for ONT Data
GEs                     The genetic elements data
GEs_hg38                The genetic elements data of GRCh38 Genome
                        Reference
getWholeChromosomes     Get whole chromosomes from methylation data
joinReplicates          Joins together two GRange objects in a single
                        containing all the replicates
mergeDMRsIteratively    Merge DMRs iteratively
mergePMDsIteratively    Merge PMDs iteratively
methylationDataList     The methylation data list
ont_gr_GM18870_chr1_PMD_bins_1k
                        Partially Methilated Domains example
ont_gr_GM18870_chr1_sorted_bins_1k
                        The ONT methylation data example
ontSampleGRangesList    The ONT 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
PMDsBinsCG              The PMDs between GM18501 and GM18876 using Bins
                        method
PMDsNoiseFilterCG       The PMDs between GM18501 and GM18876 using
                        Noise_filter method
poolMethylationDatasets
                        Pool methylation data
poolTwoMethylationDatasets
                        Pool two methylation datasets
readBismark             Read Bismark
readBismarkPool         Read Bismark pool
readONTbam              Load ONT BAM, decode MM/ML, and count modified
                        vs. unmodified reads
saveBismark             Save Bismark
scanBamChr1Random5      The bam file from ONT nanopore .pod5 files
selectCytosine          Select Cytosine Positions
syntheticDataReplicates
                        Simulated data for biological replicates
