[,mutSignExposures,numeric,ANY,ANY-method
                        Subset a mutSignExposures-class object.
[,mutationCounts,numeric,ANY,ANY-method
                        Subset a mutationCounts-class object.
[,mutationSignatures,numeric,ANY,ANY-method
                        Subset a mutationSignatures-class object.
as.data.frame,mutSignExposures-method
                        Convert and/or transpose a mutSignExposures
                        object to data.frame.
as.data.frame,mutationCounts-method
                        Convert a mutationCounts object to data.frame.
as.data.frame,mutationSignatures-method
                        Convert a mutationSignatures object to
                        data.frame.
as.list,mutFrameworkParams-method
                        Convert a mutFrameworkParams object to list.
as.list,mutationSignatures-method
                        Convert a mutationSignatures object to list.
as.matrix,mutationCounts-method
                        Convert a mutationCounts object to matrix.
as.mutation.counts      Method as.mutation.counts.
as.mutation.signatures
                        Method as.mutation.signatures.
as.mutsign.exposures    Method as.mutsign.exposures.
attachContext           Attach Nucleotide Context.
attachMutType           Attach Mutation Types.
cbind2                  Combine two mutationSignatures-class objects.
coerceObj               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.
getFwkParam             Method getFwkParam.
getMutationTypes        Method getMutationTypes.
getSampleIdentifiers    Method getSampleIdentifiers.
getSignatureIdentifiers
                        Method getSignatureIdentifiers.
importVCFfiles          Import Mutation data from VCF files.
matchSignatures         Match Mutational Signatures.
msigPlot                Method msigPlot.
mutFrameworkParams-class
                        Class mutFrameworkParams.
mutSigData              Input Data and Examples for Running Mutational
                        Signatures Analyses
mutSignExposures-class
                        Class mutSignExposures.
mutSignatures-package   Decipher Mutational Signatures from Somatic
                        Mutational Catalogs.
mutationCounts-class    Class mutationCounts.
mutationSignatures-class
                        Class mutationSignatures.
plotMutTypeProfile      Plot Mutation Signature Profiles.
plotSignExposures       Plot Signature Exposure Profiles.
prelimProcessAssess     Run a Preliminary Process Assess analysis.
processVCFdata          Process VCF data.
removeMismatchMut       Remove Mismatched Mutations.
resolveMutSignatures    Resolve Mutation Signatures.
revCompl                Compute Reverse Complement sequences.
setFwkParam             Method setFwkParam.
setMutClusterParams     Set Parameters for Extracting Mutational
                        Signatures.
show,mutFrameworkParams-method
                        Show method of the mutFrameworkParams Class.
show,mutSignExposures-method
                        Show method of the mutSignExposures Class.
show,mutationCounts-method
                        Show method of the mutationCounts Class.
show,mutationSignatures-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.
