# Decipher Mutational Signatures from Somatic Mutational Catalogs

## 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.