dami82/mutSignatures_dev
Decipher Mutational Signatures from Somatic Mutational Catalogs

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Source code
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dami82/mutSignatures_dev: Decipher Mutational Signatures from Somatic Mutational Catalogs
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API

API for dami82/mutSignatures_dev
Decipher Mutational Signatures from Somatic Mutational Catalogs

Global functions
[,mutSignExposures,numeric,ANY,ANY-method Man page Man page
[,mutationCounts,numeric,ANY,ANY-method Man page Man page
[,mutationSignatures,numeric,ANY,ANY-method Man page Man page
[-methods Man page
addWeak Man page
alexaNMF Man page Source code
as.data.frame,mutSignExposures-method Man page Man page
as.data.frame,mutationCounts-method Man page Man page
as.data.frame,mutationSignatures-method Man page Man page
as.data.frame-methods Man page
as.list,mutFrameworkParams-method Man page Man page
as.list,mutationSignatures-method Man page Man page
as.list-methods Man page
as.matrix,ANY-method Man page
as.matrix,AtomicList-method Man page
as.matrix,CompressedHitsList-method Man page
as.matrix,DataFrame-method Man page
as.matrix,DelayedArray-method Man page
as.matrix,Hits-method Man page
as.matrix,HitsList-method Man page
as.matrix,Matrix-method Man page
as.matrix,MultipleAlignment-method Man page
as.matrix,PairwiseAlignmentsSingleSubject-method Man page
as.matrix,Ranges-method Man page
as.matrix,Vector-method Man page
as.matrix,Views-method Man page
as.matrix,ViewsList-method Man page
as.matrix,XStringQuality-method Man page
as.matrix,XStringSet-method Man page
as.matrix,XStringViews-method Man page
as.matrix,mutationCounts-method Man page Man page
as.matrix-methods Man page
as.mutation.counts Man page
as.mutation.counts,data.frame-method Man page
as.mutation.counts-methods Man page
as.mutation.signatures Man page
as.mutation.signatures,data.frame-method Man page
as.mutation.signatures-methods Man page
as.mutsign.exposures Man page
as.mutsign.exposures,data.frame-method Man page
as.mutsign.exposures-methods Man page
attachContext Man page Source code
attachMutType Man page Source code
bootstrapCancerGenomes Man page
cbind2,mutationSignatures,mutationSignatures-method Man page Man page
cbind2-methods Man page
chihJenNMF Man page Source code
coerceObj Man page
coerceObj,data.frame,character-method Man page
coerceObj,mutFrameworkParams,character-method Man page Man page
coerceObj,mutSignExposures,character-method Man page Man page
coerceObj,mutationCounts,character-method Man page Man page
coerceObj,mutationSignatures,character-method Man page Man page
coerceObj-methods Man page
countMutTypes Man page Source code
decipherMutationalProcesses Man page
deconvoluteMutCounts Man page
evaluateStability Man page
extractSignatures Man page
extractXvarlinkData Man page Source code
filterOutIterations Man page
filterSNV Man page Source code
frequencize Man page Source code
getCosmicSignatures Man page Source code
getCounts Man page
getCounts,mutationCounts-method Man page Man page
getCounts-methods Man page
getFwkParam Man page
getFwkParam,mutFrameworkParams,character-method Man page Man page
getFwkParam-methods Man page
getMutationTypes Man page
getMutationTypes,mutationCounts-method Man page Man page
getMutationTypes,mutationSignatures-method Man page Man page
getMutationTypes-methods Man page
getSampleIdentifiers Man page
getSampleIdentifiers,mutSignExposures-method Man page Man page
getSampleIdentifiers,mutationCounts-method Man page Man page
getSampleIdentifiers-methods Man page
getSignatureIdentifiers Man page
getSignatureIdentifiers,mutSignExposures-method Man page Man page
getSignatureIdentifiers,mutationSignatures-method Man page Man page
getSignatureIdentifiers-methods Man page
getTestRunArgs Man page
importVCFfiles Man page Source code
initialize,mutFrameworkParams-method Man page Man page
initialize,mutSignExposures-method Man page Man page
initialize,mutationCounts-method Man page Man page
initialize,mutationSignatures-method Man page Man page
initialize-methods Man page
leadZeros Man page
matchSignatures Man page Source code
mutFrameworkParams-class Man page
mutSignExposures-class Man page
mutSignatures Man page
mutSignatures-package Man page
mutationCounts-class Man page
mutationSignatures-class Man page
plot,ANY,ANY-method Man page
plot,NMFList,missing-method Man page
plot,NMFfit,missing-method Man page
plot,color,ANY-method Man page
plot,mutSignExposures,ANY-method Man page Man page
plot,mutationCounts,ANY-method Man page Man page
plot,mutationExposure,ANY-method Man page
plot,mutationSignatures,ANY-method Man page Man page
plot,profile.mle,missing-method Man page
plot-methods Man page
plotMutCount Man page Source code
plotMutTypeProfile Man page Source code
prelimProcessAssess Man page Source code
print,ANY-method Man page
print,diagonalMatrix-method Man page
print,mutFrameworkParams-method Man page Man page
print,mutSignExposures-method Man page Man page
print,mutationCounts-method Man page Man page
print,mutationExposure-method Man page
print,mutationSignatures-method Man page Man page
print,sparseMatrix-method Man page
print-methods Man page
processVCFdata Man page Source code
removeMismatchMut Man page Source code
removeWeak Man page
resolveMutSignatures Man page Source code
revCompl Man page
setFwkParam Man page
setFwkParam,mutFrameworkParams-method Man page Man page
setFwkParam-methods Man page
setMutClusterParams Man page Source code
show,mutFrameworkParams-method Man page Man page
show,mutSignExposures-method Man page Man page
show,mutationCounts-method Man page Man page
show,mutationSignatures-method Man page Man page
show-methods Man page
silhouetteMLB Man page
simplifySignatures Man page Source code
sortByMutations Man page Source code
table2df Man page Source code
dami82/mutSignatures_dev documentation built on May 17, 2019, 7:02 p.m.

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