Man pages for mskcc/tempoSig
Maximum Likelihood Fitting of Mutational Catalogs and De Novo Inference of Signatures
| bnmf | Bayesian NMF inference of count matrix |
| catalog-tempoSig-method | Accessor for catalog |
| cosineSimilarity | Cosine similarity |
| dinucleotides | Dinucleotide labels |
| expos-tempoSig-method | Accessor for exposure |
| extractSig | Infer Signature Proportions |
| filterExposure | Filter exposures using p-values |
| filterFP | Filter False Positives |
| fitMLE | Maximum likelihood inference of signature proportions |
| kstar | Determine optimal rank |
| logLik-tempoSig-method | Accessor for logLik |
| maf2cat | Generate Mutation Catalog from MAF file |
| maf2cat3 | Construct catalog matix from MAF file (without of Ref_Tri... |
| misc-tempoSig-method | Accessor for misc |
| mutationalCone | Refit spectra using MutationalCone |
| nmf | NMF Iteration |
| pgnmf | piggyback NMF |
| plotExposure | Plot exposure |
| plot_M80 | Plot M80 Estimate |
| powerEstimate | Estimate Power for Signature Detection |
| powerPlot | Mutation load prediction plot |
| pvalue-tempoSig-method | Accessor for p-values |
| readMAFforcat | Read MAF file and Fix Chromosome Names |
| Row2Column | Reformat spectra to column-major |
| run_tSig | Wrapper Function |
| senspec | True and false positive rates |
| show-tempoSig-method | Display 'tempoSig' object |
| signat-tempoSig-method | Accessor for signature |
| sigplot | Plot signature profile |
| simulateSpectra | Simulate mutational spectra |
| tempoSig | Create 'tempoSig' object |
| tempoSig-class | Class 'tempoSig' for storing catalog and exposure |
| tmb-tempoSig-method | Accessor for TMB |
| trinucleotides | Trinucleotide labels |
| writeExposure | Write Exposure |
