.detect.footprints      Detects TF and nucleosome footprints enriched
                        in a single partition
AggregateFootprints     Gather equivalent footprints by overlaps (and
                        TF identity) under the same index
AnnotateFootprints      Annotate detected TF footprints with
                        user-provided TF motif annotations
Arrange_TFBSs_clusters
                        Convenience function to arrange a list of given
                        TFBSs into clusters
BaitCapture             Bait capture efficiency
BinMethylation          Summarize methylation inside sorting bins
CallContextMethylation
                        Call Context Methylation
CollapseStrands         Collapse strands
CollapseStrandsSM       Collapse strands in single molecule matrix
CollectCompositeData    Collect bulk SMF data for later composite
                        plotting
CompositeMethylationCorrelation
                        Composite Methylation Rate
CompositePlot           Plot composite SMF data
ConversionRate          Conversion rate
CoverageFilter          Filter Cs for coverage
Create_MethylationCallingWindows
                        Create methylation calling windows to call
                        context methylation in one run for clusters
                        lying proximally to each other
DetectExperimentType    Detect type of experiment
DetectFootprints        Wrapper to run the function detect.footprint
                        across all clusters computed over a single
                        locus
FilterByConversionRate
                        Calculate reads conversion rate
FilterContextCytosines
                        Filter Cytosines in context
FootprintCharter        Run FootprintCharter
GRanges_to_DF           Manipulate GRanges into data.frame
GetQuasRprj             Get QuasRprj
GetSingleMolMethMat     Get Single Molecule methylation matrix
HierarchicalClustering
                        Perform Hierarchical clustering on single reads
LowCoverageMethRate_RMSE
                        Low Coverage Methylation Rate RMSE
MaskSNPs                Utility function to remove cytosines whose
                        MTase target genomic context is affected by
                        SNPs
MethSM.to.MethGR        Compute MethGR from MethSM
MethSM.to.dense         Turn sparse single molecule matrix to dense
PlotAvgSMF              Plot average methylation
PlotFootprints          Plot bulk SMF separately for each partition
                        alognside footprint detection results.
PlotSM                  Wrapper for PlotSingleMoleculeStack function
PlotSingleMoleculeStack
                        Plot single molecule stack
PlotSingleSiteSMF       Plot SMF data at single site
Plot_FootprintCharter_SM
                        Plot single molecule heatmaps of footprint
                        detection results
Plot_LowCoverageMethRate
                        Plot low coverage methylation rate
Plot_LowCoverageMethRate_RMSE
                        Plot Low Coverage Methylation Rate RMSE
RollingMean             Compute rolling mean
SingleTFStateQuantificationPlot
                        Single TF state quantification bar
SingleTFStates          Hard-coded interpretation of biological states
                        from single TF sorting
SortReads               Sort reads by single TF
SortReadsBySingleTF     Wrapper to SortReads for single TF case
SortReadsBySingleTF_MultiSiteWrapper
                        Convenience wrapper to sort single molecule
                        according to TFBS clusters at multiple sites in
                        the genome
SortReadsByTFCluster    Wrapper to SortReads for TF cluster case
SortReadsByTFCluster_MultiSiteWrapper
                        Convenience wrapper to sort single molecule
                        according to TFBS clusters at multiple sites in
                        the genome
StateQuantification     Convenience for calculating state frequencies
StateQuantificationBySingleTF
                        Convenience for calculating state frequencies
                        after sorting reads by single TF
StateQuantificationByTFPair
                        Convenience for calculating state frequencies
                        after sorting reads by TF pair
StateQuantificationPlot
                        Plot states quantification bar
SubsetGRangesForSamples
                        Subset Granges for given samples
TFPairStateQuantificationPlot
                        TF pair state quantification bar
TFPairStates            Design states for TF pair case
cbind_fill_sparseMatrix
                        Implementation performing a similar operation
                        of rbind_fill_sparseMatrix but for columns
colMeans_drop0          Calculate colMeans after dropping zeros
fill.empty.columns      Fills empty columns
filter.dense.matrix     Filters dense matrix
filter_reads_from_MethGR
                        Recalculate *_T and *_M values in MethGR object
                        after filtering reads e.g. for conversion rate
full.join.granges       Utility function to perform the dplyr full_join
                        operation on GRanges object
matrix.sliding.window.average
                        Computes rolling mean
panel.cor               Utility for
                        HighCoverage_MethRate_SampleCorrelation
panel.hist              Utility for
                        HighCoverage_MethRate_SampleCorrelation
panel.jet               Utility for
                        HighCoverage_MethRate_SampleCorrelation
rbind_fill_sparseMatrix
                        Implementation performing a similar operation
                        of the plyr function rbind.fill.matrix but for
                        sparseMatrix
rowMeans_drop0          Calculate rowMeans after dropping zeros
