Man pages for dami82/mutSignatures_dev
Decipher Mutational Signatures from Somatic Mutational Catalogs

addWeakAdd Weak Mutation Types
alexaNMFPerform NMF According to Brunet Algorithm Methods for Function '' ~~
as.list-methods~~ Methods for Function 'as.list' ~~
as.matrix-methods~~ Methods for Function 'as.matrix' ~~
as.mutation.countsCoerce to Mutation Counts Object
as.mutation.counts-methods~~ Methods for Function 'as.mutation.counts' ~~
as.mutation.signaturesCoerce to Mutation Signature Object
as.mutation.signatures-methods~~ Methods for Function 'as.mutation.signatures' ~~
as.mutsign.exposuresCoerce Data Frame to Mutation Signature Exposures Object
as.mutsign.exposures-methods~~ Methods for Function 'as.mutsign.exposures' ~~
attachContextAttach Context
attachMutTypeAttach Mutation Type
bootstrapCancerGenomesBootstrap Cancer Genomes
cbind2-methods~~ Methods for Function 'cbind2' ~~
chihJenNMFAlternative NMF Algorithm
coerceObjCoerce Data Objects To Different Class
coerceObj-methods~~ Methods for Function 'coerceObj' ~~
countMutTypesCount Mutation Types
decipherMutationalProcessesDecipher Mutational Processes
deconvoluteMutCountsDeconvolute Mutation Counts
evaluateStabilityEvaluate Stability
extractSignaturesExtract Signatures
extractXvarlinkDataExtract Data From XVarLink Fields
filterOutIterationsFilter Out Iterations
filterSNVFilter Single Nucleotide Variants
frequencizeConvert Counts to Frequencies
getCosmicSignaturesRetrieve COSMIC Mutational Signatures
getCountsGet Counts from mutSignature Object
getCounts-methods~~ Methods for Function 'getCounts' ~~
getFwkParamGet Param Value from mutSignature Object
getFwkParam-methods~~ Methods for Function 'getFwkParam' ~~
getMutationTypesGet Mutation Types from mutSignature Object
getMutationTypes-methods~~ Methods for Function 'getMutationTypes' ~~
getSampleIdentifiersGet Sample Identifiers from mutSignature Object
getSampleIdentifiers-methods~~ Methods for Function 'getSampleIdentifiers' ~~
getSignatureIdentifiersGet Signature Identifier from mutSignature Object
getSignatureIdentifiers-methods~~ Methods for Function 'getSignatureIdentifiers' ~~
getTestRunArgsBuild mutSignature Objects for Examples
importVCFfilesImport VCF Files
initialize-methods~~ Methods for Function 'initialize' ~~
leadZerosAdd Leading Zeros to Numbers
matchSignaturesMatch Mutation Signatures
mutationCounts-classClass '"mutationCounts"'
mutationSignatures-classClass '"mutationSignatures"'
mutFrameworkParams-classClass '"mutFrameworkParams"'
mutSignatures-packageDecipher Mutational Signatures from Somatic Mutational...
mutSignExposures-classClass '"mutSignExposures"'
plot-methods~~ Methods for Function 'plot' ~~
plotMutCountPlot Mutation Counts
plotMutTypeProfilePlot a Mutation Profile
prelimProcessAssessAssess Preliminary Processes
print-methods~~ Methods for Function 'print' ~~
processVCFdataProcess VCF Files
removeMismatchMutRemove Mutations Corresponding to Mismatched Reference...
removeWeakRemove Uncommon Mutation Types
resolveMutSignaturesResolve Mutation Signatures
revComplReverse Complement of a Nucleic Acid Sequence
setFwkParamSet or Adjust Single Framework Parameters
setFwkParam-methods~~ Methods for Function 'setFwkParam' ~~
setMutClusterParamsSet Mutation Cluster Parameters
show-methods~~ Methods for Function 'show' ~~
silhouetteMLBRun a Silhouette Analysis Similar to Matlab
simplifySignaturesSimplify Extended Signatures
sortByMutationsSort Object By Mutation Type
table2dfConvert Matrix to Data Frame
z[-methods~~ Methods for Function '[' ~~
dami82/mutSignatures_dev documentation built on May 17, 2019, 7:02 p.m.