Decipher Mutational Signatures from Somatic Mutational Catalogs

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Documentation for package ‘mutSignatures’ version 2.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

mutSignatures-package	Decipher Mutational Signatures from Somatic Mutational Catalogs.
as.data.frame-method	Convert and/or transpose a mutSignExposures object to data.frame.
as.data.frame-method	Convert a mutationCounts object to data.frame.
as.data.frame-method	Convert a mutationSignatures object to data.frame.
as.list-method	Convert a mutFrameworkParams object to list.
as.list-method	Convert a mutationSignatures object to list.
as.matrix-method	Convert a mutationCounts object to matrix.
as.mutation.counts	Method as.mutation.counts.
as.mutation.counts-method	Method as.mutation.counts.
as.mutation.signatures	Method as.mutation.signatures.
as.mutation.signatures-method	Method as.mutation.signatures.
as.mutsign.exposures	Method as.mutsign.exposures.
as.mutsign.exposures-method	Method as.mutsign.exposures.
attachContext	Attach Nucleotide Context.
attachMutType	Attach Mutation Types.
cbind2	Combine two mutationSignatures-class objects.
cbind2-method	Combine two mutationSignatures-class objects.
coerceObj	Method coerceObj.
coerceObj-method	Method coerceObj.
countMutTypes	Count Mutation Types.
decipherMutationalProcesses	Decipher Mutational Processes Contributing to a Collection of Genomic Mutations.
extractXvarlinkData	Extract Variants from XvarlinkData.
filterSNV	Filter Single Nucleotide Variants.
frequencize	Convert Mutation COunts to PerMille Frequencies.
getCosmicSignatures	Obtain COSMIC mutational Signatures.
getCounts	Method getCounts.
getCounts-method	Method getCounts.
getFwkParam	Method getFwkParam.
getFwkParam-method	Method getFwkParam.
getMutationTypes	Method getMutationTypes.
getMutationTypes-method	Method getMutationTypes.
getSampleIdentifiers	Method getSampleIdentifiers.
getSampleIdentifiers-method	Method getSampleIdentifiers.
getSignatureIdentifiers	Method getSignatureIdentifiers.
getSignatureIdentifiers-method	Method getSignatureIdentifiers.
importVCFfiles	Import Mutation data from VCF files.
initialize-method	Class mutFrameworkParams.
initialize-method	Class mutSignExposures.
initialize-method	Class mutationCounts.
initialize-method	Class mutationSignatures.
matchSignatures	Match Mutational Signatures.
msigPlot	Method msigPlot.
msigPlot-method	Method msigPlot.
mutationCounts-class	Class mutationCounts.
mutationSignatures-class	Class mutationSignatures.
mutFrameworkParams-class	Class mutFrameworkParams.
mutSigData	Input Data and Examples for Running Mutational Signatures Analyses
mutSignExposures-class	Class mutSignExposures.
plotMutTypeProfile	Plot Mutation Signature Profiles.
plotSignExposures	Plot Signature Exposure Profiles.
prelimProcessAssess	Run a Preliminary Process Assess analysis.
print-method	Show method of the mutFrameworkParams Class.
print-method	Show method of the mutSignExposures Class.
print-method	Show method of the mutationCounts Class.
print-method	Show method of the mutationSignatures Class.
processVCFdata	Process VCF data.
removeMismatchMut	Remove Mismatched Mutations.
resolveMutSignatures	Resolve Mutation Signatures.
revCompl	Compute Reverse Complement sequences.
setFwkParam	Method setFwkParam.
setFwkParam-method	Method setFwkParam.
setMutClusterParams	Set Parameters for Extracting Mutational Signatures.
show-method	Show method of the mutFrameworkParams Class.
show-method	Show method of the mutSignExposures Class.
show-method	Show method of the mutationCounts Class.
show-method	Show method of the mutationSignatures Class.
silhouetteMLB	Silhouette Analysis.
simplifySignatures	Simplify Mutational Signatures.
sortByMutations	Sort Data by Mutation Type.
table2df	Table Mutation Types by Sample.
[-method	Subset a mutSignExposures-class object.
[-method	Subset a mutationCounts-class object.
[-method	Subset a mutationSignatures-class object.