# Generated by roxygen2 (4.1.0): do not edit by hand

export("alleleCounts<-")
export("genotype<-")
export(ASEsetFromCountList)
export(RBias)
export(alleleCounts)
export(arank)
export(barplotLatticeCounts)
export(barplotLatticeFraction)
export(countsPerSample)
export(countsPerSnp)
export(coverageMatrixListFromGAL)
export(decorateWithExons)
export(decorateWithGenes)
export(defaultMapBias)
export(detectAI)
export(fraction)
export(frequency)
export(genotype)
export(getAlleleCounts)
export(getAnnotationDataFrame)
export(getAreaFromGeneNames)
export(getCDSFromAnnotation)
export(getCDSVector)
export(getDefaultMapBiasExpMean)
export(getExonsFromAnnotation)
export(getExonsVector)
export(getGenesFromAnnotation)
export(getGenesVector)
export(getSnpIdFromLocation)
export(getTranscriptsFromAnnotation)
export(getTranscriptsVector)
export(hetPerSample)
export(hetPerSnp)
export(impBamGAL)
export(impBamGRL)
export(impBcfGR)
export(impBcfGRL)
export(implodeList)
export(mapBias)
export(realCigarPosition)
export(realCigarPositions)
export(realCigarPositionsList)
export(refbiasByAnnotation)
export(scanForHeterozygotes)
exportClasses(ASEset)
exportClasses(ReferenceBias)
exportMethods("alleleCounts<-")
exportMethods("genotype<-")
exportMethods(ASEDAnnotationTrack)
exportMethods(CoverageDataTrack)
exportMethods(alleleCounts)
exportMethods(arank)
exportMethods(barplot)
exportMethods(binom.test)
exportMethods(chisq.test)
exportMethods(countsPerSample)
exportMethods(countsPerSnp)
exportMethods(defaultMapBias)
exportMethods(detectAI)
exportMethods(fraction)
exportMethods(frequency)
exportMethods(genotype)
exportMethods(glocationplot)
exportMethods(hetFilt)
exportMethods(hetPerSample)
exportMethods(hetPerSnp)
exportMethods(inferAlleles)
exportMethods(inferGenotypes)
exportMethods(lbarplot)
exportMethods(locationplot)
exportMethods(mapBias)
exportMethods(refAllele)
exportMethods(refFraction)
exportMethods(refbiasByAnnotation)
exportMethods(show)
import(BiocGenerics)
import(GenomeInfoDb)
import(S4Vectors)
import(grid)
import(methods)
importClassesFrom(AnnotationDbi,AnnotationDb)
importClassesFrom(AnnotationDbi,ChipDb)
importClassesFrom(AnnotationDbi,GODb)
importClassesFrom(AnnotationDbi,InparanoidDb)
importClassesFrom(AnnotationDbi,OrgDb)
importClassesFrom(AnnotationDbi,ReactomeDb)
importClassesFrom(GenomicAlignments,GAlignmentPairs)
importClassesFrom(GenomicAlignments,GAlignments)
importClassesFrom(GenomicAlignments,GAlignmentsList)
importClassesFrom(GenomicFeatures,TxDb)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(GenomicRanges,GRangesList)
importClassesFrom(Gviz,AnnotationTrack)
importClassesFrom(Gviz,DataTrack)
importClassesFrom(Gviz,DetailsAnnotationTrack)
importClassesFrom(Gviz,GeneRegionTrack)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,select)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,append)
importFrom(Biostrings,subseq)
importFrom(GenomicAlignments,GAlignmentPairs)
importFrom(GenomicAlignments,GAlignments)
importFrom(GenomicAlignments,GAlignmentsList)
importFrom(GenomicAlignments,cigar)
importFrom(GenomicAlignments,cigarToRleList)
importFrom(GenomicAlignments,cigarWidthAlongReferenceSpace)
importFrom(GenomicAlignments,pileLettersAt)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignmentPairsFromBam)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,readGAlignmentsFromBam)
importFrom(GenomicFeatures,'isActiveSeq<-')
importFrom(GenomicFeatures,cds)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,isActiveSeq)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,"assays<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,SummarizedExperiment)
importFrom(GenomicRanges,assays)
importFrom(GenomicRanges,colData)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,grglist)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,rowData)
importFrom(GenomicRanges,unlist)
importFrom(Gviz,AnnotationTrack)
importFrom(Gviz,DataTrack)
importFrom(Gviz,DetailsAnnotationTrack)
importFrom(Gviz,GeneRegionTrack)
importFrom(Gviz,plotTracks)
importFrom(IRanges,IRanges)
importFrom(IRanges,IntervalTree)
importFrom(IRanges,coverage)
importFrom(IRanges,ranges)
importFrom(IRanges,resize)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,unlist)
importFrom(IRanges,which)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,BcfFile)
importFrom(Rsamtools,BcfFileList)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,ScanBcfParam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,indexBcf)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,scanBamWhat)
importFrom(Rsamtools,scanBcf)
importFrom(Rsamtools,scanFa)
importFrom(Rsamtools,scanFaIndex)
importFrom(graphics,barplot)
importFrom(graphics,plot)
importFrom(lattice,barchart)
importFrom(lattice,trellis.par.set)
importFrom(methods,show)
importMethodsFrom(AnnotationDbi,columns)
