characterToBSGenome	characterToBSGenome
circularRandomizeRegions	circularRandomizeRegions
commonRegions	commonRegions
createFunctionsList	createFunctionsList
createRandomRegions	createRandomRegions
emptyCacheRegioneR	emptyCacheRegioneR
extendRegions	extendRegions
filterChromosomes	filterChromosomes
getChromosomesByOrganism	getChromosomesByOrganism
getGenome	getGenome
getGenomeAndMask	getGenomeAndMask
getMask	getMask
joinRegions	joinRegions
listChrTypes	listChrTypes
localZScore	localZScore
maskFromBSGenome	maskFromBSGenome
meanDistance	meanDistance
meanInRegions	meanInRegions
mergeRegions	mergeRegions
numOverlaps	numOverlaps
overlapGraphicalSummary	overlapGraphicalSummary
overlapPermTest	overlapPermTest
overlapRegions	overlapRegions
permTest	permTest
plot.localZScoreResults	plot.localZScoreResults
plot.localZScoreResultsList	plot.localZScoreResultsList
plot.permTestResults	plot.permTestResults
plot.permTestResultsList	plot.permTestResultsList
plotRegions	plotRegions
print.permTestResults	print.permTestResults
randomizeRegions	randomizeRegions
recomputePermTest	recomputePermTest
resampleRegions	resampleRegions
splitRegions	splitRegions
subtractRegions	subtractRegions
summary.permTestResults	summary.permTestResults
summary.permTestResultsList	summary.permTestResultsList
toDataframe	toDataframe
toGRanges	toGRanges
uniqueRegions	uniqueRegions
