Man pages for pdiakumis/hrdetect
Signature Tools
| applyHRDetectDavies2017 | Apply HRDetect (Davies et al. 2017) |
| ascatToHRDLOH | HRD-LOH index from ASCAT |
| bedpeToRearrCatalogue | bedpeToRearrCatalogue |
| calc.ai | Number of Telomeric Allelic Imbalances |
| calc.hrd | HRD-LOH index |
| calc.lst | Large-scale state transitions |
| computeCorrelationOfTwoSetsOfSigs | computeCorrelationOfTwoSetsOfSigs |
| cos.sim | Cosine Similarity |
| export_SignatureFit_withBootstrap_to_JSON | Export Signature Fit with bootstrap to JSON |
| exposureDistributionBarplot | Distribution of Signatures in Samples |
| 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 |
| genomePlot | Genome Plot |
| HRDetect_pipeline | HRDetect Pipeline |
| KLD | KL-divergence |
| matchedClustering | Clustering with Matches |
| plot.CosSimSignatures | plot.CosSimSignatures |
| 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 |
| plotRearrSignatures | Plot Rearrangement Signatures or Catalogues |
| plot_SignatureFit_withBootstrap | plot_SignatureFit_withBootstrap |
| plotSubsSignatures | Plot Substitution Signatures or Catalogues |
| readTable | readTable |
| RMSE | RMSE |
| SignatureExtraction | Mutational Signatures Extraction |
| SignatureFit | Mutational Signatures Fit |
| SignatureFit_withBootstrap | Mutational Signatures Fit with Bootstrap |
| SignatureFit_withBootstrap_Analysis | Mutational Signatures Fit with Bootstrap Analysis |
| sortCatalogue | Sort 96-channel Substitution Catalogues |
| tabToIndelsClassification | tab to Indels Classification |
| tabToSNVcatalogue | TAB to SNV Catalogue |
| unexplainedSamples | Estimate samples not fully explained by signature fit |
| vcfToIndelsClassification | VCF to Indels Classification |
| vcfToSNVcatalogue | VCF to SNV catalogue |
| writeTable | writeTable |
