# Generated by roxygen2: do not edit by hand

export("qcFilters<-")
export("qcLog<-")
export(ConcordanceRule)
export(ISNVFilter)
export(WithinHostExperiment)
export(adaptiveFilter)
export(annotateCodonChange)
export(annotateGenes)
export(asViralBottleneckInput)
export(benchmarkCallers)
export(buildSFS)
export(buildSFSList)
export(calcCallerConcordance)
export(calcDiversity)
export(calcNeutralityTests)
export(calcSharedVariants)
export(chao1ISNV)
export(checkDiversityPlausibility)
export(compareDiversity)
export(compareSFS)
export(consensusISNV)
export(consensusSequences)
export(correctSFSBias)
export(detectCrossContamination)
export(detectEmergingVariants)
export(estimateSelectionCoefficient)
export(exactBottleneck)
export(exportPairFrequencies)
export(fitDiversityModel)
export(flagISNV)
export(flagPrimerSites)
export(flagReplicateDiscordance)
export(flagStrandBiasSCI)
export(flagTemporalInconsistency)
export(fusFs)
export(multitestCorrection)
export(neutralityFromSFS)
export(pNpSWithinHost)
export(passedISNV)
export(permutationTest)
export(piISNV)
export(plotFrequencySpectrum)
export(plotFrequencyTrajectory)
export(plotPairScatter)
export(plotQCDashboard)
export(plotSFS)
export(qcFilters)
export(qcLog)
export(qcSummary)
export(quickBottleneck)
export(readWithinHost)
export(readWithinHostTable)
export(sciStrandBias)
export(shannonISNV)
export(simpsonISNV)
export(tajimaD)
export(trackFrequency)
export(transmissionPairs)
export(wattersonISNV)
exportClasses(ConcordanceRule)
exportClasses(ISNVFilter)
exportClasses(WithinHostExperiment)
exportClasses(WithinHostSFS)
exportMethods("[")
exportMethods("qcFilters<-")
exportMethods("qcLog<-")
exportMethods(annotateCodonChange)
exportMethods(annotateGenes)
exportMethods(calcDiversity)
exportMethods(calcNeutralityTests)
exportMethods(combineCols)
exportMethods(combineRows)
exportMethods(consensusSequences)
exportMethods(flagISNV)
exportMethods(pNpSWithinHost)
exportMethods(passedISNV)
exportMethods(qcFilters)
exportMethods(qcLog)
exportMethods(show)
exportMethods(transmissionPairs)
importClassesFrom(Biostrings,DNAStringSet)
importClassesFrom(Biostrings,XString)
importClassesFrom(GenomicFeatures,TxDb)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(GenomicRanges,GRangesList)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importClassesFrom(VariantAnnotation,VCF)
importFrom(BiocGenerics,ncol)
importFrom(BiocGenerics,nrow)
importFrom(BiocGenerics,strand)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,extractAt)
importFrom(Biostrings,replaceAt)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,subseq)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,extractTranscriptSeqs)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,start)
importFrom(IRanges,"end<-")
importFrom(IRanges,"start<-")
importFrom(IRanges,CharacterList)
importFrom(IRanges,IRanges)
importFrom(IRanges,IntegerList)
importFrom(IRanges,end)
importFrom(IRanges,start)
importFrom(IRanges,width)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,combineCols)
importFrom(S4Vectors,combineRows)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,VRanges)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,expand)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,header)
importFrom(VariantAnnotation,info)
importFrom(VariantAnnotation,predictCoding)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,ref)
importFrom(VariantAnnotation,samples)
importFrom(graphics,hist)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(stats,as.formula)
importFrom(stats,chisq.test)
importFrom(stats,coef)
importFrom(stats,dbeta)
importFrom(stats,dbinom)
importFrom(stats,kruskal.test)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pbeta)
importFrom(stats,pbinom)
importFrom(stats,pnorm)
importFrom(stats,quantile)
importFrom(stats,residuals)
importFrom(stats,terms)
importFrom(stats,update)
importFrom(stats,wilcox.test)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
