# Generated by roxygen2: do not edit by hand

export(advancedArg)
export(analyzeChr)
export(annotateRegions)
export(calculatePvalues)
export(calculateStats)
export(coerceGR)
export(collapseFullCoverage)
export(coverageToExon)
export(createBw)
export(createBwSample)
export(define_cluster)
export(extendedMapSeqlevels)
export(filterData)
export(findRegions)
export(fullCoverage)
export(getRegionCoverage)
export(getTotalMapped)
export(loadCoverage)
export(makeGenomicState)
export(makeModels)
export(mergeResults)
export(preprocessCoverage)
export(railMatrix)
export(rawFiles)
export(regionMatrix)
export(sampleDepth)
import(S4Vectors)
importFrom(BiocGenerics,path)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpworkers)
importFrom(GenomeInfoDb,'seqlengths<-')
importFrom(GenomeInfoDb,mapSeqlevels)
importFrom(GenomeInfoDb,renameSeqlevels)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicFeatures,'isActiveSeq<-')
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,isActiveSeq)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicFiles,reduceByFile)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,tileGenome)
importFrom(Hmisc,wtd.quantile)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IRanges)
importFrom(IRanges,IntegerList)
importFrom(IRanges,RleList)
importFrom(IRanges,Views)
importFrom(IRanges,end)
importFrom(IRanges,nrow)
importFrom(IRanges,ranges)
importFrom(IRanges,reduce)
importFrom(IRanges,runLength)
importFrom(IRanges,slice)
importFrom(IRanges,start)
importFrom(IRanges,width)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(bumphunter,annotateTranscripts)
importFrom(bumphunter,locfitByCluster)
importFrom(bumphunter,matchGenes)
importFrom(bumphunter,runmedByCluster)
importFrom(derfinderHelper,fstats.apply)
importFrom(methods,formalArgs)
importFrom(methods,is)
importFrom(qvalue,qvalue)
importFrom(rtracklayer,BigWigFile)
importFrom(rtracklayer,BigWigFileList)
importFrom(stats,qf)
importFrom(stats,runif)
importFrom(utils,browseURL)
importMethodsFrom(AnnotationDbi,select)
importMethodsFrom(GenomicFeatures,promoters)
importMethodsFrom(GenomicRanges,'$')
importMethodsFrom(GenomicRanges,'$<-')
importMethodsFrom(GenomicRanges,'[')
importMethodsFrom(GenomicRanges,'[<-')
importMethodsFrom(GenomicRanges,'names<-')
importMethodsFrom(GenomicRanges,'strand<-')
importMethodsFrom(GenomicRanges,as.data.frame)
importMethodsFrom(GenomicRanges,countOverlaps)
importMethodsFrom(GenomicRanges,coverage)
importMethodsFrom(GenomicRanges,disjoin)
importMethodsFrom(GenomicRanges,findOverlaps)
importMethodsFrom(GenomicRanges,gaps)
importMethodsFrom(GenomicRanges,isDisjoint)
importMethodsFrom(GenomicRanges,length)
importMethodsFrom(GenomicRanges,names)
importMethodsFrom(GenomicRanges,reduce)
importMethodsFrom(GenomicRanges,resize)
importMethodsFrom(GenomicRanges,sort)
importMethodsFrom(GenomicRanges,strand)
importMethodsFrom(GenomicRanges,width)
importMethodsFrom(IRanges,'[')
importMethodsFrom(IRanges,'[<-')
importMethodsFrom(IRanges,'[[')
importMethodsFrom(IRanges,'[[<-')
importMethodsFrom(IRanges,'colnames<-')
importMethodsFrom(IRanges,as.data.frame)
importMethodsFrom(IRanges,cbind)
importMethodsFrom(IRanges,colnames)
importMethodsFrom(IRanges,lapply)
importMethodsFrom(IRanges,length)
importMethodsFrom(IRanges,mean)
importMethodsFrom(IRanges,median)
importMethodsFrom(IRanges,names)
importMethodsFrom(IRanges,ncol)
importMethodsFrom(IRanges,nrow)
importMethodsFrom(IRanges,order)
importMethodsFrom(IRanges,quantile)
importMethodsFrom(IRanges,rbind)
importMethodsFrom(IRanges,relist)
importMethodsFrom(IRanges,sum)
importMethodsFrom(IRanges,unlist)
importMethodsFrom(IRanges,which)
importMethodsFrom(Rsamtools,names)
importMethodsFrom(rtracklayer,export)
importMethodsFrom(rtracklayer,import)
importMethodsFrom(rtracklayer,import.bw)
