Man pages for dami82/mutSignatures_dev
Decipher Mutational Signatures from Somatic Mutational Catalogs
| addWeak | Add Weak Mutation Types |
| alexaNMF | Perform NMF According to Brunet Algorithm |
| as.data.frame-methods | ~~ Methods for Function 'as.data.frame' ~~ |
| as.list-methods | ~~ Methods for Function 'as.list' ~~ |
| as.matrix-methods | ~~ Methods for Function 'as.matrix' ~~ |
| as.mutation.counts | Coerce to Mutation Counts Object |
| as.mutation.counts-methods | ~~ Methods for Function 'as.mutation.counts' ~~ |
| as.mutation.signatures | Coerce to Mutation Signature Object |
| as.mutation.signatures-methods | ~~ Methods for Function 'as.mutation.signatures' ~~ |
| as.mutsign.exposures | Coerce Data Frame to Mutation Signature Exposures Object |
| as.mutsign.exposures-methods | ~~ Methods for Function 'as.mutsign.exposures' ~~ |
| attachContext | Attach Context |
| attachMutType | Attach Mutation Type |
| bootstrapCancerGenomes | Bootstrap Cancer Genomes |
| cbind2-methods | ~~ Methods for Function 'cbind2' ~~ |
| chihJenNMF | Alternative NMF Algorithm |
| coerceObj | Coerce Data Objects To Different Class |
| coerceObj-methods | ~~ Methods for Function 'coerceObj' ~~ |
| countMutTypes | Count Mutation Types |
| decipherMutationalProcesses | Decipher Mutational Processes |
| deconvoluteMutCounts | Deconvolute Mutation Counts |
| evaluateStability | Evaluate Stability |
| extractSignatures | Extract Signatures |
| extractXvarlinkData | Extract Data From XVarLink Fields |
| filterOutIterations | Filter Out Iterations |
| filterSNV | Filter Single Nucleotide Variants |
| frequencize | Convert Counts to Frequencies |
| getCosmicSignatures | Retrieve COSMIC Mutational Signatures |
| getCounts | Get Counts from mutSignature Object |
| getCounts-methods | ~~ Methods for Function 'getCounts' ~~ |
| getFwkParam | Get Param Value from mutSignature Object |
| getFwkParam-methods | ~~ Methods for Function 'getFwkParam' ~~ |
| getMutationTypes | Get Mutation Types from mutSignature Object |
| getMutationTypes-methods | ~~ Methods for Function 'getMutationTypes' ~~ |
| getSampleIdentifiers | Get Sample Identifiers from mutSignature Object |
| getSampleIdentifiers-methods | ~~ Methods for Function 'getSampleIdentifiers' ~~ |
| getSignatureIdentifiers | Get Signature Identifier from mutSignature Object |
| getSignatureIdentifiers-methods | ~~ Methods for Function 'getSignatureIdentifiers' ~~ |
| getTestRunArgs | Build mutSignature Objects for Examples |
| importVCFfiles | Import VCF Files |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
| leadZeros | Add Leading Zeros to Numbers |
| matchSignatures | Match Mutation Signatures |
| mutationCounts-class | Class '"mutationCounts"' |
| mutationSignatures-class | Class '"mutationSignatures"' |
| mutFrameworkParams-class | Class '"mutFrameworkParams"' |
| mutSignatures-package | Decipher Mutational Signatures from Somatic Mutational... |
| mutSignExposures-class | Class '"mutSignExposures"' |
| plot-methods | ~~ Methods for Function 'plot' ~~ |
| plotMutCount | Plot Mutation Counts |
| plotMutTypeProfile | Plot a Mutation Profile |
| prelimProcessAssess | Assess Preliminary Processes |
| print-methods | ~~ Methods for Function 'print' ~~ |
| processVCFdata | Process VCF Files |
| removeMismatchMut | Remove Mutations Corresponding to Mismatched Reference... |
| removeWeak | Remove Uncommon Mutation Types |
| resolveMutSignatures | Resolve Mutation Signatures |
| revCompl | Reverse Complement of a Nucleic Acid Sequence |
| setFwkParam | Set or Adjust Single Framework Parameters |
| setFwkParam-methods | ~~ Methods for Function 'setFwkParam' ~~ |
| setMutClusterParams | Set Mutation Cluster Parameters |
| show-methods | ~~ Methods for Function 'show' ~~ |
| silhouetteMLB | Run a Silhouette Analysis Similar to Matlab |
| simplifySignatures | Simplify Extended Signatures |
| sortByMutations | Sort Object By Mutation Type |
| table2df | Convert Matrix to Data Frame |
| z[-methods | ~~ Methods for Function '[' ~~ |
