Man pages for Nik-Zainal-Group/signature.tools.lib
signature.tools.lib
| applyHRDetectDavies2017 | Apply HRDetect (Davies et al. 2017) |
| ascatToHRDLOH | HRD-LOH index from ASCAT |
| assignSignatureProbabilityToMutations | Assign Signature Probability to Mutations |
| bedpeToRearrCatalogue | bedpeToRearrCatalogue |
| calc.ai | Number of Telomeric Allelic Imbalances |
| calc.hrd | HRD-LOH index |
| calc.lst | Large-scale state transitions |
| cataloguesClustering | Clustering of Catalogues or Signatures |
| combineStrandBiasResults | combine Transcription and Replication strand bias results |
| computeCorrelationOfTwoSetsOfSigs | computeCorrelationOfTwoSetsOfSigs |
| computeCorrelation_parallel | Compute Correlation (parallel) |
| convertExposuresFromOrganToRefSigs | convertExposuresFromOrganToRefSigs |
| convertExposuresFromOrganToRefSigsIfAny | convertExposuresFromOrganToRefSigsIfAny |
| convertToAlexandrovChannels | Convert DNV catalogues from Zou's to Alexandrov's style |
| cos_sim | Cosine Similarity |
| dnvTabToDNVcatalogue | Build a Dinucleotide Variants Catalogue from DNVs list |
| dnvTabToTNVcatalogue | Build a Triinucleotide Variants Catalogue from DNVs |
| evaluatePerformanceExposures | evaluate performance exposures |
| evaluatePerformanceExposuresList | evaluate performance exposures list |
| evaluatePerformanceSignatureSimilarity | evaluate performance signature similarity |
| evaluatePerformanceSignatureSimilarityList | evaluate performance signature similarity list |
| expandColumnToMatrix | Expand columns to matrix |
| export_SignatureFit_withBootstrap_to_JSON | Export Signature Fit with bootstrap to JSON |
| exposureDistributionBarplot | Distribution of Signatures in Samples |
| finaliseCommonRareSignatureExposures | Finalise Common and Rare Signature Exposures |
| findClosestCOSMIC30 | Find closest COSMIC30 signatures |
| findClosestCOSMIC30andCombinations | Find closest COSMIC30 signatures or combination of COSMIC30 |
| findClosestCOSMIC30andCombinations_withSimilarity | Find closest COSMIC30 signatures or combination of COSMIC30 |
| findClosestCOSMIC30_withSimilarity | Find closest COSMIC30 signatures |
| findContextSNV | Find SNV context |
| findKataegis | find kataegis |
| Fit | Signature Fit |
| fitMerge | Selecting and merging signature fit results from Multi-Step... |
| FitMS | Multi-Step Mutational Signatures Fit |
| fitMStoJSON | Export the results from the FitMS function to JSON |
| fitSignaturesWithSignatures | fitSignaturesWithSignatures |
| fitToJSON | Export the results from the Fit function to JSON |
| genomeChart | genomeChart |
| genomeChartSV | genomeChartSV |
| genomePlot | Genome Plot |
| getCOSMICSignatures | getCOSMICSignatures |
| getGiniThresholds | Get Gini Thresholds |
| getOrganSignatures | getOrganSignatures |
| getReferenceSignatures | getReferenceSignatures |
| getSignaturesForFitting | getSignaturesForFitting |
| HRDetect_pipeline | HRDetect Pipeline |
| KLD | KL-divergence |
| loadFitFromFile | Load fit object from file |
| loadSimulatedData | Load simulated data |
| matchedClustering | Clustering with Matches |
| mutationSampling | mutationSampling |
| oddRatio | Odd Ratio |
| plotContextSNV | plot SNV context |
| plotCopyNumbers | plot Copy Numbers from ASCAT-like file |
| plotCosSimSignatures | plotCosSimSignatures |
| plotDNVSignatures | Plot Dinucleotide Variant Signatures or Catalogues |
| plotDNVSignaturesCompact | Plot Dinucleotide Variant Signatures or Catalogues, Compact... |
| plotFit | Plot the results from the Fit function |
| plotFitMS | Plot the results from the FitMS function |
| plotFitResults | Plot the results from the Fit or FitMS function |
| plotGenericSignatures | Plot Generic Signatures or Catalogues |
| plot_HRDetect_BootstrapScores | plot_HRDetect_BootstrapScores |
| plot_HRDetect_Contributions | plot_HRDetect_Contributions |
| plot_HRDetect_overall | plot_HRDetect_overall |
| plot_HRDLOH_HRDetect_Contributions | plot_HRDLOH_HRDetect_Contributions |
| plotJunctionsCatalogues | Plot Junctions Catalogues |
| plotMatrix | Plot Matrix |
| plotRearrSignatures | Plot Rearrangement Signatures or Catalogues |
| plotRegion | plotRegion |
| plot_SignatureFit_withBootstrap | plot_SignatureFit_withBootstrap |
| plotSignatures | Plot Signatures with automated detection of type of mutations |
| plotStrandBiasResults | plot Transcription and Replication strand bias results |
| plotSubsSignatures | Plot Substitution Signatures or Catalogues |
| plotSubsSignaturesCompact | Plot Substitution Signatures or Catalogues, Compact plot |
| plotTNVcatalogues | Plot Tinucleotide Variant Signatures or Catalogues |
| rareSignatureExtraction | Rare Signatures Extraction |
| readTable | readTable |
| RMSE | RMSE |
| sampleStrandBias | Transcription and Replication strand bias for a sample |
| saveFitToFile | Save fit object to file |
| saveSimulatedData | Save simulated data |
| SignatureExtraction | Mutational Signatures Extraction |
| SignatureFit | Mutational Signatures Fit (deprecated) |
| signatureFit_pipeline | Signature fit pipeline |
| SignatureFit_withBootstrap | Mutational Signatures Fit with Bootstrap (deprecated) |
| SignatureFit_withBootstrap_Analysis | Mutational Signatures Fit with Bootstrap Analysis |
| simpleCatalogueSimulation | simpleCatalogueSimulation |
| snvTabToDNVcatalogue | Build a Dinucleotide Variants Catalogue from SNVs |
| sortCatalogue | Sort 96-channel Substitution Catalogues |
| tabToDNVcatalogue | TAB to DNV catalogue |
| tabToIndelsClassification | tab to Indels Classification |
| tabToSNVcatalogue | TAB to SNV Catalogue |
| tnvTabToTNVcatalogue | Build a Trinucleotide Variants Catalogue from TNVs list |
| unexplainedSamples | Estimate samples not fully explained by the given signatures |
| updateSigNamesWithMatchTable | update signature names using a match table |
| vcfToDNVcatalogue | VCF to DNV catalogue |
| vcfToIndelsClassification | VCF to Indels Classification |
| vcfToSNVcatalogue | VCF to SNV catalogue |
| writeFitResultsToJSON | Write the results from the Fit or FitMS function to JSON |
| writeTable | writeTable |
