# Generated by roxygen2: do not edit by hand

S3method(ConvertToPSelf,GInteractions)
S3method(ConvertToPSelf,default)
S3method(PeaksToGRanges,PSFit)
S3method(PeaksToGRanges,default)
S3method(PeaksToNarrowPeak,PSFit)
S3method(PeaksToNarrowPeak,default)
S3method(TagsToGInteractions,PSFit)
S3method(TagsToGInteractions,default)
S3method(exportPeaks,PSFit)
S3method(exportPeaks,default)
S3method(plot,PInter)
S3method(plot,PIntra)
S3method(plot,PSFit)
S3method(plot,PSelf)
S3method(summary,PInter)
S3method(summary,PIntra)
S3method(summary,PSFit)
S3method(summary,PSelf)
export(AnalysisStatistics)
export(ConvertToPE_BAM)
export(ConvertToPSelf)
export(MACPETUlt)
export(PeaksToGRanges)
export(PeaksToNarrowPeak)
export(TagsToGInteractions)
export(exportPeaks)
exportClasses(PInter)
exportClasses(PIntra)
exportClasses(PSFit)
exportClasses(PSelf)
import(Rcpp)
importClassesFrom(Biostrings,BStringSet)
importClassesFrom(Biostrings,DNAStringSet)
importClassesFrom(GenomeInfoDb,Seqinfo)
importClassesFrom(GenomicAlignments,GAlignmentPairs)
importClassesFrom(GenomicAlignments,GAlignments)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(IRanges,IRanges)
importClassesFrom(InteractionSet,GInteractions)
importClassesFrom(Rsamtools,BamFile)
importClassesFrom(Rsamtools,ScanBamParam)
importClassesFrom(S4Vectors,Annotated)
importClassesFrom(ShortRead,FastqStreamer)
importClassesFrom(ShortRead,SFastqQuality)
importClassesFrom(ShortRead,SRFilterResult)
importClassesFrom(ShortRead,ShortReadQ)
importClassesFrom(intervals,Intervals)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpworkers)
importFrom(Biostrings,BStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,intersect)
importFrom(Biostrings,width)
importFrom(GEOquery,gunzip)
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,last)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,seqinfo)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,IRanges)
importFrom(IRanges,narrow)
importFrom(InteractionSet,GInteractions)
importFrom(InteractionSet,anchors)
importFrom(InteractionSet,findOverlaps)
importFrom(InteractionSet,pairdist)
importFrom(Rbowtie,bowtie)
importFrom(Rbowtie,bowtie_build)
importFrom(Rcpp,evalCpp)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asBam)
importFrom(Rsamtools,asSam)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,mergeBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,scanBamWhat)
importFrom(Rsamtools,sortBam)
importFrom(Rsamtools,testPairedEndBam)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,sort)
importFrom(ShortRead,FastqStreamer)
importFrom(ShortRead,countLines)
importFrom(ShortRead,writeFastq)
importFrom(ShortRead,yield)
importFrom(futile.logger,appender.tee)
importFrom(futile.logger,flog.appender)
importFrom(futile.logger,flog.info)
importFrom(futile.logger,flog.layout)
importFrom(futile.logger,flog.warn)
importFrom(futile.logger,layout.format)
importFrom(gtools,mixedsort)
importFrom(intervals,Intervals)
importFrom(intervals,clusters)
importFrom(intervals,interval_included)
importFrom(intervals,size)
importFrom(knitr,kable)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(plyr,.)
importFrom(plyr,ddply)
importFrom(plyr,dlply)
importFrom(plyr,ldply)
importFrom(plyr,llply)
importFrom(rbamtools,bamReader)
importFrom(rbamtools,readerToFastq)
importFrom(rtracklayer,export)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,ppois)
importFrom(utils,methods)
importFrom(utils,write.table)
useDynLib(MACPET)
