# Association analysis of genomic regions based on permutation tests

## Documentation for package ‘regioneR’ version 1.40.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
resampleGenome | resampleGenome
resampleRegions | Resample Regions
splitRegions | Split Regions
subtractRegions | Subtract Regions
toDataframe | toDataframe
toGRanges | toGRanges
uniqueRegions | Unique Regions