# Generated by roxygen2: do not edit by hand

export("alleleCounts<-")
export("alt<-")
export("aquals<-")
export("genotype<-")
export("mapBias<-")
export("phase<-")
export("ref<-")
export(ASEDAnnotationTrack)
export(ASEsetFromArrays)
export(ASEsetFromBam)
export(ASEsetFromCountList)
export(CoverageDataTrack)
export(DetectedAIFromArray)
export(GAnalysis)
export(RiskVariantFromGRangesAndPhaseArray)
export(alleleCounts)
export(alt)
export(altExist)
export(annotationBarplot)
export(aquals)
export(arank)
export(barplotLatticeCounts)
export(barplotLatticeFraction)
export(basic)
export(countAllelesFromBam)
export(countsPerSample)
export(countsPerSnp)
export(coverageMatrixListFromGAL)
export(decorateWithExons)
export(decorateWithGenes)
export(defaultMapBias)
export(defaultPhase)
export(detectAI)
export(detectedAI_vs_threshold_variable_multigraph_plot)
export(detectedAI_vs_threshold_variable_plot)
export(detectedAI_vs_threshold_variable_summary)
export(fraction)
export(fractionPlotDf)
export(frequency)
export(frequency_vs_threshold_variable_multigraph_plot)
export(frequency_vs_threshold_variable_plot)
export(frequency_vs_threshold_variable_summary)
export(gba)
export(genotype)
export(genotype2phase)
export(getAlleleCounts)
export(getAlleleQuality)
export(getAnnotationDataFrame)
export(getAreaFromGeneNames)
export(getCDSFromAnnotation)
export(getCDSVector)
export(getDefaultMapBiasExpMean)
export(getDefaultMapBiasExpMean3D)
export(getExonsFromAnnotation)
export(getExonsVector)
export(getGenesFromAnnotation)
export(getGenesVector)
export(getSnpIdFromLocation)
export(getTranscriptsFromAnnotation)
export(getTranscriptsVector)
export(hetFilt)
export(impBamGAL)
export(impBamGRL)
export(impBcfGR)
export(impBcfGRL)
export(implodeList.old)
export(legendBarplot)
export(locationplot)
export(lva)
export(lva.internal)
export(makeMaskedFasta)
export(mapBias)
export(mapBiasRef)
export(maternalAllele)
export(minCountFilt)
export(minFreqFilt)
export(multiAllelicFilt)
export(paternalAllele)
export(phase)
export(phase2genotype)
export(phaseArray2phaseMatrix)
export(phaseMatrix2Array)
export(pvalue)
export(randomRef)
export(realCigarPosition.old)
export(realCigarPositions.old)
export(realCigarPositionsList.old)
export(ref)
export(refExist)
export(referenceFrequency)
export(reference_frequency_density_vs_threshold_variable_multigraph_plot)
export(reference_frequency_density_vs_threshold_variable_plot)
export(regionSummary)
export(scanForHeterozygotes)
export(scanForHeterozygotes.old)
export(sumnames)
export(thresholdCountSample)
export(thresholdDeltaFrequency)
export(thresholdFrequency)
export(thresholdPvalue)
export(usedSNPs_vs_threshold_variable_summary)
exportClasses(ASEset)
exportClasses(DetectedAI)
exportClasses(GlobalAnalysis)
exportClasses(LinkVariantAlmlof)
exportClasses(RegionSummary)
exportClasses(RiskVariant)
exportMethods("alleleCounts<-")
exportMethods("alt<-")
exportMethods("aquals<-")
exportMethods("genotype<-")
exportMethods("mapBias<-")
exportMethods("phase<-")
exportMethods("ref<-")
exportMethods(ASEDAnnotationTrack)
exportMethods(ASEsetFromBam)
exportMethods(alleleCounts)
exportMethods(alt)
exportMethods(altExist)
exportMethods(aquals)
exportMethods(arank)
exportMethods(barplot)
exportMethods(basic)
exportMethods(binom.test)
exportMethods(chisq.test)
exportMethods(countAllelesFromBam)
exportMethods(countsPerSample)
exportMethods(countsPerSnp)
exportMethods(coverageMatrixListFromGAL)
exportMethods(defaultMapBias)
exportMethods(defaultPhase)
exportMethods(detectAI)
exportMethods(detectedAI_vs_threshold_variable_multigraph_plot)
exportMethods(detectedAI_vs_threshold_variable_plot)
exportMethods(detectedAI_vs_threshold_variable_summary)
exportMethods(fraction)
exportMethods(fractionPlotDf)
exportMethods(frequency)
exportMethods(frequency_vs_threshold_variable_multigraph_plot)
exportMethods(frequency_vs_threshold_variable_plot)
exportMethods(frequency_vs_threshold_variable_summary)
exportMethods(gba)
exportMethods(gbarplot)
exportMethods(genotype)
exportMethods(genotype2phase)
exportMethods(getAlleleCounts)
exportMethods(getAlleleQuality)
exportMethods(getAreaFromGeneNames)
exportMethods(getDefaultMapBiasExpMean)
exportMethods(getDefaultMapBiasExpMean3D)
exportMethods(getSnpIdFromLocation)
exportMethods(glocationplot)
exportMethods(hetFilt)
exportMethods(impBamGAL)
exportMethods(impBcfGR)
exportMethods(impBcfGRL)
exportMethods(inferAlleles)
exportMethods(inferAltAllele)
exportMethods(inferGenotypes)
exportMethods(locationplot)
exportMethods(lva)
exportMethods(lva.internal)
exportMethods(makeMaskedFasta)
exportMethods(mapBias)
exportMethods(mapBiasRef)
exportMethods(maternalAllele)
exportMethods(minCountFilt)
exportMethods(minFreqFilt)
exportMethods(multiAllelicFilt)
exportMethods(paternalAllele)
exportMethods(phase)
exportMethods(phase2genotype)
exportMethods(phaseArray2phaseMatrix)
exportMethods(phaseMatrix2Array)
exportMethods(plot)
exportMethods(pvalue)
exportMethods(randomRef)
exportMethods(ref)
exportMethods(refAllele)
exportMethods(refExist)
exportMethods(referenceFrequency)
exportMethods(reference_frequency_density_vs_threshold_variable_multigraph_plot)
exportMethods(reference_frequency_density_vs_threshold_variable_plot)
exportMethods(regionSummary)
exportMethods(scanForHeterozygotes)
exportMethods(sumnames)
exportMethods(thresholdCountSample)
exportMethods(thresholdDeltaFrequency)
exportMethods(thresholdFrequency)
exportMethods(thresholdPvalue)
exportMethods(usedSNPs_vs_threshold_variable_summary)
import(BiocGenerics)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(SummarizedExperiment)
import(grid)
import(methods)
importClassesFrom(AnnotationDbi,AnnotationDb)
importClassesFrom(AnnotationDbi,ChipDb)
importClassesFrom(AnnotationDbi,GODb)
importClassesFrom(AnnotationDbi,OrgDb)
importClassesFrom(AnnotationDbi,ReactomeDb)
importClassesFrom(GenomicAlignments,GAlignmentPairs)
importClassesFrom(GenomicAlignments,GAlignments)
importClassesFrom(GenomicAlignments,GAlignmentsList)
importClassesFrom(GenomicFeatures,TxDb)
importClassesFrom(Gviz,AnnotationTrack)
importClassesFrom(Gviz,DataTrack)
importClassesFrom(Gviz,DetailsAnnotationTrack)
importClassesFrom(Gviz,GeneRegionTrack)
importClassesFrom(Gviz,GenomeAxisTrack)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,select)
importFrom(Biostrings,DNAStringSet)
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,readGAlignments)
importFrom(GenomicFeatures,'isActiveSeq<-')
importFrom(GenomicFeatures,cds)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,isActiveSeq)
importFrom(GenomicFeatures,transcripts)
importFrom(Gviz,AnnotationTrack)
importFrom(Gviz,DataTrack)
importFrom(Gviz,DetailsAnnotationTrack)
importFrom(Gviz,GeneRegionTrack)
importFrom(Gviz,GenomeAxisTrack)
importFrom(Gviz,plotTracks)
importFrom(Rsamtools,ApplyPileupsParam)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,BcfFile)
importFrom(Rsamtools,BcfFileList)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,PileupFiles)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,ScanBcfParam)
importFrom(Rsamtools,applyPileups)
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(VariantAnnotation,'alt<-')
importFrom(VariantAnnotation,'ref<-')
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,ref)
importFrom(grDevices,heat.colors)
importFrom(graphics,abline)
importFrom(graphics,barplot)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,plot)
importFrom(graphics,plot.default)
importFrom(graphics,points)
importFrom(graphics,symbols)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(gridExtra,grid.arrange)
importFrom(lattice,barchart)
importFrom(lattice,levelplot)
importFrom(lattice,panel.abline)
importFrom(lattice,panel.barchart)
importFrom(lattice,panel.linejoin)
importFrom(lattice,panel.smoothScatter)
importFrom(lattice,panel.text)
importFrom(lattice,trellis.par.set)
importFrom(lattice,xyplot)
importFrom(latticeExtra,doubleYScale)
importFrom(nlme,lme)
importFrom(seqinr,write.fasta)
importFrom(stats,anova)
importFrom(stats,dist)
importFrom(stats,formula)
importFrom(stats,lm)
importFrom(stats,setNames)
importMethodsFrom(AnnotationDbi,columns)
importMethodsFrom(BSgenome,snpsByOverlaps)
