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| 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 |