decompTumor2Sig-package	decompTumor2Sig-package
addBestSignatureToSubset	addBestSignatureToSubset
adjustAlexandrovSignature	adjustAlexandrovSignature
adjustShiraishiSignature	adjustShiraishiSignature
adjustSignaturesForRegionSet	adjustSignaturesForRegionSet
buildGenomesFromMutationData	buildGenomesFromMutationData
buildSortedAlexandrovSignaturePatternList	buildSortedAlexandrovSignaturePatternList
compNucFreq	compNucFreq
composeGenomesFromExposures	composeGenomesFromExposures
computeExplainedVariance	computeExplainedVariance
computeFrobeniusNorm	computeFrobeniusNorm
computeRSS	computeRSS
convAlx2Shi	convAlx2Shi
convertAlexandrov2Shiraishi	convertAlexandrov2Shiraishi
convertGenomesFromVRanges	convertGenomesFromVRanges
convertSeqFreqToBaseFreq	convertSeqFreqToBaseFreq
decomposeTumorGenomes	decomposeTumorGenomes
decompTumor2Sig	decompTumor2Sig-package
determineSignatureDistances	determineSignatureDistances
determineTypeNumBasesAndTrDir	determineTypeNumBasesAndTrDir
downgradeShiraishiSignatures	downgradeShiraishiSignatures
evaluateDecompositionQuality	evaluateDecompositionQuality
getBestDecomp4Ksignatures	getBestDecomp4Ksignatures
getCountData	getCountData
getFeatVectList	getFeatVectList
getGenomesFromMutFeatData	getGenomesFromMutFeatData
getNumFlankingBases	getNumFlankingBases
getNumSignatures	getNumSignatures
getSampleList	getSampleList
getSigFeatDist	getSigFeatDist
getSigFromEstParam	getSigFromEstParam
getSignaturesFromEstParam	getSignaturesFromEstParam
getSigType	getSigType
haveTrDir	haveTrDir
is.probability.data.frame	is.probability.data.frame
is.probability.data.frame.list	is.probability.data.frame.list
is.probability.matrix	is.probability.matrix
is.probability.matrix.list	is.probability.matrix.list
is.probability.object	is.probability.object
is.probability.vector	is.probability.vector
is.probability.vector.list	is.probability.vector.list
isAlexandrovSet	isAlexandrovSet
isBackGround	isBackGround
isEstParamObject	isEstParamObject
isExposureSet	isExposureSet
isMutFeatDataObject	isMutFeatDataObject
isShiraishiSet	isShiraishiSet
isSignatureSet	isSignatureSet
mapSignatureSets	mapSignatureSets
plotAlexandrovModel	plotAlexandrovModel
plotDecomposedContribution	plotDecomposedContribution
plotExplainedVariance	plotExplainedVariance
plotMutationDistribution	plotMutationDistribution
plotShiraishiModel	plotShiraishiModel
processMultipleSigSets	processMultipleSigSets
QPforSig	QPforSig
readAlexandrovSignatures	readAlexandrovSignatures
readGenomesFromMPF	readGenomesFromMPF
readGenomesFromVCF	readGenomesFromVCF
readShiraishiSignatures	readShiraishiSignatures
roundIntegerSum	roundIntegerSum
sameSignatureFormat	sameSignatureFormat
setNames4ShiraishiTable	setNames4ShiraishiTable
setNumFlankingBases	setNumFlankingBases
setSigFeatDist	setSigFeatDist
setSigType	setSigType
setTrDir	setTrDir
