Man pages for mutSignatures
Decipher Mutational Signatures from Somatic Mutational Catalogs
| addWeak | Add Weak Mutation TYpes |
| alexaNMF | Perform Non-negative Matrix Factorization using Brunet's... |
| 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.data.frame-mutSignExposures-method | Convert and/or transpose a mutSignExposures object to... |
| as.list-mutationSignatures-method | Convert a mutationSignatures object to list. |
| as.list-mutFrameworkParams-method | Convert a mutFrameworkParams 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. |
| bootstrapCancerGenomes | Bootstrap a Mutation Count Matrix. |
| cbind2 | Combine two mutationSignatures-class objects. |
| chihJenNMF | Perform Non-negative Matrix Factorization using Chih-Jen... |
| coerceObj-methods | Method coerceObj. |
| countMutTypes | Count Mutation Types. |
| custom_cssls | Custom CSSLS. |
| custom_fcnnls | Custom Fast Combinatorial Nonnegative Least-Square. |
| decipherMutationalProcesses | Decipher Mutational Processes Contributing to a Collection of... |
| deconvoluteMutCounts | Deconvolute Mutation Counts. |
| evaluateStability | Evaluate Results Stability. |
| extractSignatures | Extract Signatures from Genomic Mutational Catalogs. |
| extractXvarlinkData | Extract Variants from XvarlinkData. |
| filterOutIterations | Remove Iterations that Generated Outlier Results. |
| 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. |
| getTestRunArgs | Generate Arguments for Running Examples and Mock Runs. |
| importVCFfiles | Import Mutation data from VCF files. |
| leadZeros | Add Leading Zeros to Numbers. |
| matchSignatures | Match Mutational Signatures. |
| msigPlot | Method msigPlot. |
| mutationCounts-class | Class mutationCounts. |
| mutationCounts-show | Show method of the mutationCounts Class. |
| mutationSignatures-class | Class mutationSignatures. |
| mutationSignatures-show | Show method of the mutationSignatures Class. |
| mutFrameworkParams-class | Class mutFrameworkParams. |
| mutFrameworkParams-show | Show method of the mutFrameworkParams Class. |
| mutSigData | Input Data and Examples for Running Mutational Signatures... |
| mutSignatures-package | Decipher Mutational Signatures from Somatic Mutational... |
| mutSignExposures-class | Class mutSignExposures. |
| mutSignExposures-show | Show method of the mutSignExposures Class. |
| 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. |
| removeWeak | Remove Mutation Types Not Meeting the Threshold. |
| resolveMutSignatures | Resolve Mutation Signatures. |
| revCompl | Compute Reverse Complement sequences. |
| setFwkParam | Method setFwkParam. |
| setMutClusterParams | Set Parameters for Extracting Mutational Signatures. |
| silhouetteMLB | Silhouette Analysis. |
| simplifySignatures | Simplify Mutational Signatures. |
| sortByMutations | Sort Data by Mutation Type. |
| sub-mutationCounts-numeric-ANY-ANY-method | Subset a mutationCounts-class object. |
| sub-mutationSignatures-numeric-ANY-ANY-method | Subset a mutationSignatures-class object. |
| sub-mutSignExposures-numeric-ANY-ANY-method | Subset a mutSignExposures-class object. |
| table2df | Table Mutation Types by Sample. |
