characterToBSGenome     characterToBSGenome
circularRandomizeRegions
                        Circular Randomize Regions
commonRegions           Common Regions
createFunctionsList     Create Functions List
createRandomRegions     Create Random Regions
emptyCacheRegioneR      Empty Cache regioneR
extendRegions           Extend Regions
filterChromosomes       filterChromosomes
getChromosomesByOrganism
                        getChromosomesByOrganism
getGenome               getGenome
getGenomeAndMask        getGenomeAndMask
getMask                 getMask
joinRegions             Join Regions
listChrTypes            filterChromosomes listChrTypes
localZScore             Local z-score
maskFromBSGenome        maskFromBSGenome
meanDistance            Mean Distance
meanInRegions           Mean In Regions
mergeRegions            Merge Regions
numOverlaps             Number Of Overlaps
overlapGraphicalSummary
                        Overlap Graphical Summary
overlapPermTest         Permutation Test for Overlap
overlapRegions          Overlap Regions
permTest                Permutation Test
plot.localZScoreResults
                        Plot localZscore results
plot.permTestResults    Function for plotting the results from a
                        'permTestResults' object.
plot.permTestResultsList
                        Function for plotting the results from a
                        'permTestResultsList' object when more than one
                        evaluation function was used.
plotRegions             Plot Regions
randomizeRegions        Randomize Regions
recomputePermTest       Recompute Permutation Test
resampleRegions         Resample Regions
splitRegions            Split Regions
subtractRegions         Subtract Regions
toDataframe             toDataframe
toGRanges               toGRanges
uniqueRegions           Unique Regions
