WithinHostExperiment-package	WithinHostExperiment-package
.ConcordanceRule	ConcordanceRule-class
.ISNVFilter	ISNVFilter-class
.WithinHostExperiment	WithinHostExperiment-class
.WithinHostSFS	WithinHostSFS-class
adaptiveFilter	adaptiveFilter
annotateCodonChange	annotateCodonChange
annotateCodonChange,WithinHostExperiment,ANY,character-method	annotateCodonChange
annotateCodonChange,WithinHostExperiment,ANY,XString-method	annotateCodonChange
annotateCodonChange,WithinHostExperiment,character,DNAStringSet-method	annotateCodonChange
annotateCodonChange,WithinHostExperiment,GRanges,DNAStringSet-method	annotateCodonChange
annotateCodonChange,WithinHostExperiment,GRangesList,DNAStringSet-method	annotateCodonChange
annotateCodonChange,WithinHostExperiment,TxDb,DNAStringSet-method	annotateCodonChange
annotateGenes	annotateGenes
annotateGenes,WithinHostExperiment,GRanges-method	annotateGenes
annotateGenes,WithinHostExperiment,TxDb-method	annotateGenes
asViralBottleneckInput	asViralBottleneckInput
benchmarkCallers	benchmarkCallers
buildSFS	buildSFS
buildSFSList	buildSFSList
calcCallerConcordance	calcCallerConcordance
calcDiversity	calcDiversity
calcDiversity,WithinHostExperiment-method	calcDiversity
calcNeutralityTests	calcNeutralityTests
calcNeutralityTests,WithinHostExperiment-method	calcNeutralityTests
calcSharedVariants	calcSharedVariants
chao1ISNV	chao1ISNV
checkDiversityPlausibility	checkDiversityPlausibility
coerce,VCF,WithinHostExperiment-method	coerce-WHE
coerce,VRanges,WithinHostExperiment-method	coerce-WHE
coerce,WithinHostExperiment,data.frame-method	coerce-WHE
coerce,WithinHostExperiment,VRanges-method	coerce-WHE
coerce-WHE	coerce-WHE
combineCols,WithinHostExperiment-method	WHE-combine
combineRows,WithinHostExperiment-method	WHE-combine
compareDiversity	compareDiversity
compareSFS	compareSFS
ConcordanceRule	ConcordanceRule
ConcordanceRule-class	ConcordanceRule-class
consensusISNV	consensusISNV
consensusSequences	consensusSequences
consensusSequences,WithinHostExperiment,character-method	consensusSequences
consensusSequences,WithinHostExperiment,DNAStringSet-method	consensusSequences
consensusSequences,WithinHostExperiment,XString-method	consensusSequences
correctSFSBias	correctSFSBias
detectCrossContamination	detectCrossContamination
detectEmergingVariants	detectEmergingVariants
estimateSelectionCoefficient	estimateSelectionCoefficient
exactBottleneck	exactBottleneck
example_whe	example_whe
exportPairFrequencies	exportPairFrequencies
fitDiversityModel	fitDiversityModel
flagISNV	flagISNV
flagISNV,WithinHostExperiment-method	flagISNV
flagPrimerSites	flagPrimerSites
flagReplicateDiscordance	flagReplicateDiscordance
flagStrandBiasSCI	flagStrandBiasSCI
flagTemporalInconsistency	flagTemporalInconsistency
fusFs	fusFs
ISNVFilter	ISNVFilter
ISNVFilter-class	ISNVFilter-class
multitestCorrection	multitestCorrection
neutralityFromSFS	neutralityFromSFS
passedISNV	WHE-accessors
passedISNV,WithinHostExperiment-method	WHE-accessors
permutationTest	permutationTest
piISNV	piISNV
plotFrequencySpectrum	plotFrequencySpectrum
plotFrequencyTrajectory	plotFrequencyTrajectory
plotPairScatter	plotPairScatter
plotQCDashboard	plotQCDashboard
plotSFS	plotSFS
pNpSWithinHost	pNpSWithinHost
pNpSWithinHost,WithinHostExperiment,ANY,character-method	pNpSWithinHost
pNpSWithinHost,WithinHostExperiment,ANY,XString-method	pNpSWithinHost
pNpSWithinHost,WithinHostExperiment,character,DNAStringSet-method	pNpSWithinHost
pNpSWithinHost,WithinHostExperiment,GRanges,DNAStringSet-method	pNpSWithinHost
pNpSWithinHost,WithinHostExperiment,GRangesList,DNAStringSet-method	pNpSWithinHost
pNpSWithinHost,WithinHostExperiment,TxDb,DNAStringSet-method	pNpSWithinHost
qcFilters	WHE-accessors
qcFilters,WithinHostExperiment-method	WHE-accessors
qcFilters<-	WHE-accessors
qcFilters<-,WithinHostExperiment-method	WHE-accessors
qcLog	WHE-accessors
qcLog,WithinHostExperiment-method	WHE-accessors
qcLog<-	WHE-accessors
qcLog<-,WithinHostExperiment-method	WHE-accessors
qcSummary	qcSummary
quickBottleneck	quickBottleneck
readWithinHost	readWithinHost
readWithinHostTable	readWithinHostTable
sciStrandBias	sciStrandBias
shannonISNV	shannonISNV
show,ConcordanceRule-method	ConcordanceRule-class
show,ISNVFilter-method	ISNVFilter-class
show,WithinHostExperiment-method	WithinHostExperiment-class
show,WithinHostSFS-method	WithinHostSFS-class
simpsonISNV	simpsonISNV
tajimaD	tajimaD
trackFrequency	trackFrequency
transmissionPairs	WHE-accessors
transmissionPairs,WithinHostExperiment-method	WHE-accessors
wattersonISNV	wattersonISNV
WHE-combine	WHE-combine
WithinHostExperiment	WithinHostExperiment
WithinHostExperiment-class	WithinHostExperiment-class
WithinHostSFS	WithinHostSFS-class
WithinHostSFS-class	WithinHostSFS-class
[,WithinHostExperiment,ANY,ANY,ANY-method	WithinHostExperiment-class
