# Generated by roxygen2: do not edit by hand

S3method(plot,localZScoreResults)
S3method(plot,localZScoreResultsList)
S3method(plot,permTestResults)
S3method(plot,permTestResultsList)
S3method(print,permTestResults)
S3method(summary,permTestResults)
S3method(summary,permTestResultsList)
export(characterToBSGenome)
export(circularRandomizeRegions)
export(commonRegions)
export(createFunctionsList)
export(createRandomRegions)
export(emptyCacheRegioneR)
export(extendRegions)
export(filterChromosomes)
export(getChromosomesByOrganism)
export(getGenome)
export(getGenomeAndMask)
export(getMask)
export(joinRegions)
export(listChrTypes)
export(localZScore)
export(maskFromBSGenome)
export(meanDistance)
export(meanInRegions)
export(mergeRegions)
export(numOverlaps)
export(overlapGraphicalSummary)
export(overlapPermTest)
export(overlapRegions)
export(permTest)
export(plotRegions)
export(randomizeRegions)
export(recomputePermTest)
export(resampleGenome)
export(resampleRegions)
export(splitRegions)
export(subtractRegions)
export(toDataframe)
export(toGRanges)
export(uniqueRegions)
import(BSgenome)
import(GenomeInfoDb)
import(Seqinfo)
import(graphics)
import(parallel)
importFrom(Biostrings,
  collapse,
  masks
)
importFrom(GenomicRanges,
  GRanges,
  GRangesList,
  countOverlaps,
  distanceToNearest,
  elementMetadata,
  end,
  findOverlaps,
  mcols,
  reduce,
  resize,
  shift,
  start,
  tile,
  width
)
importFrom(IRanges,
  IRanges,
  tolower
)
importFrom(S4Vectors,
  Rle,
  queryHits,
  subjectHits
)
importFrom(Seqinfo,
  seqlevels,
  seqnames
)
importFrom(memoise,
  forget,
  memoise
)
importFrom(methods,
  hasArg,
  is
)
importFrom(rtracklayer,import)
importFrom(stats,
  dnorm,
  qnorm,
  rnorm,
  runif,
  sd,
  setNames
)
importFrom(tools,file_ext)
importFrom(utils,
  as.roman,
  head,
  setTxtProgressBar,
  txtProgressBar
)
