mutSignatures-package	mutSignatures-package
addWeak	addWeak
alexaNMF	alexaNMF
as.data.frame,mutationCounts-method	as.data.frame-mutationCounts-method
as.data.frame,mutationSignatures-method	as.data.frame-mutationSignatures-method
as.data.frame,mutSignExposures-method	as.data.frame-mutSignExposures-method
as.list,mutationSignatures-method	as.list-mutationSignatures-method
as.list,mutFrameworkParams-method	as.list-mutFrameworkParams-method
as.matrix,mutationCounts-method	as.matrix-mutationCounts-method
as.mutation.counts	as.mutation.counts
as.mutation.counts,data.frame,ANY,ANY-method	as.mutation.counts
as.mutation.counts,data.frame-method	as.mutation.counts
as.mutation.signatures	as.mutation.signatures
as.mutation.signatures,data.frame-method	as.mutation.signatures
as.mutsign.exposures	as.mutsign.exposures
as.mutsign.exposures,data.frame,logical-method	as.mutsign.exposures
attachContext	attachContext
attachMutType	attachMutType
bootstrapCancerGenomes	bootstrapCancerGenomes
cbind2	cbind2
cbind2,mutationSignatures,mutationSignatures-method	cbind2
chihJenNMF	chihJenNMF
coerceObj	coerceObj-methods
coerceObj,data.frame,character-method	coerceObj-methods
coerceObj,mutationCounts,character-method	coerceObj-methods
coerceObj,mutationSignatures,character-method	coerceObj-methods
coerceObj,mutFrameworkParams,character-method	coerceObj-methods
coerceObj,mutSignExposures,character-method	coerceObj-methods
countMutTypes	countMutTypes
custom_cssls	custom_cssls
custom_fcnnls	custom_fcnnls
decipherMutationalProcesses	decipherMutationalProcesses
deconvoluteMutCounts	deconvoluteMutCounts
evaluateStability	evaluateStability
extractSignatures	extractSignatures
extractXvarlinkData	extractXvarlinkData
filterOutIterations	filterOutIterations
filterSNV	filterSNV
frequencize	frequencize
getCosmicSignatures	getCosmicSignatures
getCounts	getCounts
getCounts,mutationCounts-method	getCounts
getFwkParam	getFwkParam
getFwkParam,mutFrameworkParams,character-method	getFwkParam
getMutationTypes	getMutationTypes
getMutationTypes,mutationCounts-method	getMutationTypes
getMutationTypes,mutationSignatures-method	getMutationTypes
getSampleIdentifiers	getSampleIdentifiers
getSampleIdentifiers,mutationCounts-method	getSampleIdentifiers
getSampleIdentifiers,mutSignExposures-method	getSampleIdentifiers
getSignatureIdentifiers	getSignatureIdentifiers
getSignatureIdentifiers,mutationSignatures-method	getSignatureIdentifiers
getSignatureIdentifiers,mutSignExposures-method	getSignatureIdentifiers
getTestRunArgs	getTestRunArgs
importVCFfiles	importVCFfiles
initialize,mutationCounts-method	mutationCounts-class
initialize,mutationSignatures-method	mutationSignatures-class
initialize,mutFrameworkParams-method	mutFrameworkParams-class
initialize,mutSignExposures-method	mutSignExposures-class
leadZeros	leadZeros
matchSignatures	matchSignatures
msigPlot	msigPlot
msigPlot,mutationCounts-method	msigPlot
msigPlot,mutationSignatures-method	msigPlot
msigPlot,mutSignExposures-method	msigPlot
mutationCounts-class	mutationCounts-class
mutationSignatures-class	mutationSignatures-class
mutFrameworkParams-class	mutFrameworkParams-class
mutSigData	mutSigData
mutSignExposures-class	mutSignExposures-class
plotMutTypeProfile	plotMutTypeProfile
plotSignExposures	plotSignExposures
prelimProcessAssess	prelimProcessAssess
print,mutationCounts-method	mutationCounts-show
print,mutationSignatures-method	mutationSignatures-show
print,mutFrameworkParams-method	mutFrameworkParams-show
print,mutSignExposures-method	mutSignExposures-show
processVCFdata	processVCFdata
removeMismatchMut	removeMismatchMut
removeWeak	removeWeak
resolveMutSignatures	resolveMutSignatures
revCompl	revCompl
setFwkParam	setFwkParam
setFwkParam,mutFrameworkParams,character,ANY-method	setFwkParam
setFwkParam,mutFrameworkParams,character-method	setFwkParam
setMutClusterParams	setMutClusterParams
show,mutationCounts-method	mutationCounts-show
show,mutationSignatures-method	mutationSignatures-show
show,mutFrameworkParams-method	mutFrameworkParams-show
show,mutSignExposures-method	mutSignExposures-show
silhouetteMLB	silhouetteMLB
simplifySignatures	simplifySignatures
sortByMutations	sortByMutations
table2df	table2df
[,mutationCounts,numeric-method	sub-mutationCounts-numeric-method
[,mutationSignatures,numeric-method	sub-mutationSignatures-numeric-method
[,mutSignExposures,numeric-method	sub-mutSignExposures-numeric-method
