├── .Rbuildignore ├── .gitignore ├── CINSignatureQuantification.Rproj ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── AllClasses.R ├── AllGenerics.R ├── CINSignatureQuantification.R ├── LinCombDecompSigs.R ├── addSampleFeatures.R ├── applyThreshNormAndScaling.R ├── avoidMeasurementErrors.R ├── calculateActivity.R ├── calculateActivityDrews.R ├── calculateActivityMac.R ├── calculateFeatures.R ├── calculateSampleByComponentMatrix.R ├── calculateSampleByComponentMatrixDrews.R ├── calculateSampleByComponentMatrixMac.R ├── checkChromosomeFormat.R ├── checkInputTypes.R ├── checkSegValRounding.R ├── checkbinned.R ├── clinPredictionDenovo.R ├── clinPredictionPlatinum.R ├── createCNQuant.R ├── data.R ├── dropChromosomes.R ├── extractCopynumberFeaturesDrews.R ├── extractCopynumberFeaturesMac.R ├── generateSampleFeatData.R ├── getActivities.R ├── getBPnumDrews.R ├── getBPnumMac.R ├── getCNDrews.R ├── getCNMac.R ├── getCancerSpecificSignatures.R ├── getCentromereDistCountsDrews.R ├── getCentromereDistCountsMac.R ├── getChangepointCNDrews.R ├── getChangepointCNMac.R ├── getExperiment.R ├── getFeatures.R ├── getOscillationDrews.R ├── getOscillationMac.R ├── getPloidyfeat.R ├── getSampleByComponent.R ├── getSamplefeatures.R ├── getSamples.R ├── getSegCounts.R ├── getSegTable.R ├── getSegments.R ├── getSegsizeDrews.R ├── getSegsizeMac.R ├── idSmoothingTargets.R ├── methods-CNQuant.R ├── methods-ExpQuant.R ├── methods-SigQuant.R ├── plotActivities.R ├── plotSampleByComponent.R ├── plotSegments.R ├── quantifyCNSignatures.R ├── removeQuietSamples.R ├── scaleByModel.R ├── smoothAndMergeSegments.R ├── smoothSegments.R ├── startCopynumberFeatureExtractionDrews.R ├── subsetCNfeatures.R ├── subsetSigActivities.R └── subsetfeatFitting.R ├── README.md ├── data-raw ├── cancerSpecificSignatures.R └── example_class_objects.R ├── data ├── CNobj.drews.rda ├── CNobj.mac.rda ├── Drews2022_CX3CX2_Clinical_classifier.rda ├── Drews2022_TCGA_Mixture_Models.rda ├── Drews2022_TCGA_Scaling_Variables.rda ├── Drews2022_TCGA_Signature_Thresholds.rda ├── Drews2022_TCGA_Signatures.rda ├── Macintyre2018_OV_Mixture_Models.rda ├── Macintyre2018_OV_Signatures.rda ├── Macintyre2018_OV_Signatures_normalised.rda ├── SIGobj.drews.rda ├── SIGobj.mac.rda ├── TCGA_478_Samples_SNP6_GOLD.rda ├── cancerSpecificSignatures.rda ├── gap_hg19.rda ├── gap_hg38.rda ├── hg19.chrom.sizes.rda ├── hg38.chrom.sizes.rda └── test.sample.features.rda ├── inst ├── CITATION ├── Example_data.R ├── FlexmixToRubenMethodDiff.rda └── ccs.list.RDS ├── man ├── CINSignatureQuantification.Rd ├── CNQuant-class.Rd ├── CNobj.drews.Rd ├── CNobj.mac.Rd ├── Drews2022_CX3CX2_Clinical_classifier.Rd ├── Drews2022_TCGA_Mixture_Models.Rd ├── Drews2022_TCGA_Scaling_Variables.Rd ├── Drews2022_TCGA_Signature_Thresholds.Rd ├── Drews2022_TCGA_Signatures.Rd ├── ExpQuant-class.Rd ├── Macintyre2018_OV_Mixture_Models.Rd ├── Macintyre2018_OV_Signatures.Rd ├── Macintyre2018_OV_Signatures_normalised.Rd ├── SIGobj.drews.Rd ├── SIGobj.mac.Rd ├── SigQuant-class.Rd ├── TCGA_478_Samples_SNP6_GOLD.Rd ├── addsampleFeatures.Rd ├── calculateActivity-methods.Rd ├── calculateFeatures-methods.Rd ├── calculateSampleByComponentMatrix-methods.Rd ├── cancerSpecificSignatures.Rd ├── clinPredictionDenovo-methods.Rd ├── clinPredictionPlatinum-methods.Rd ├── createCNQuant.Rd ├── gap_hg19.Rd ├── gap_hg38.Rd ├── getActivities-methods.Rd ├── getExperiment-methods.Rd ├── getFeatures-methods.Rd ├── getSampleByComponent-methods.Rd ├── getSamplefeatures-methods.Rd ├── getSamples-methods.Rd ├── getSegments-methods.Rd ├── hg19.chrom.sizes.Rd ├── hg38.chrom.sizes.Rd ├── plotActivities.Rd ├── plotSampleByComponent.Rd ├── plotSegments.Rd ├── quantifyCNSignatures-methods.Rd ├── sub-CNQuant-character-missing-method.Rd ├── sub-CNQuant-numeric-missing-method.Rd ├── sub-SigQuant-character-missing-method.Rd ├── sub-SigQuant-numeric-missing-method.Rd └── test.sample.features.Rd ├── tests ├── testthat.R └── testthat │ ├── test-addSampleFeatures.R │ ├── test-avoidMeasurementErrors.R │ ├── test-checkChromosomeFormat.R │ ├── test-checkSegValRounding.R │ ├── test-checkbinned.R │ ├── test-clinPredictionDenovo.R │ ├── test-clinPredictionPlatinum.R │ ├── test-dropChromosomes.R │ ├── test-getActivities.R │ ├── test-getExperiment.R │ ├── test-getFeatures.R │ ├── test-getPloidyfeat.R │ ├── test-getSampleByComponent.R │ ├── test-getSamplefeatures.R │ ├── test-getSamples.R │ ├── test-getSegCounts.R │ ├── test-getSegments.R │ ├── test-idSmoothingTargets.R │ ├── test-plotActivities.R │ ├── test-plotSegments.R │ ├── test-removeQuietSamples.R │ ├── test-scaleByModel.R │ ├── test-smoothAndMergeSegments.R │ ├── test-smoothSegments.R │ ├── test-subsetCNfeatures.R │ ├── test-subsetSigActivities.R │ └── test-subsetfeatFitting.R └── vignettes ├── .gitignore └── CINSignatureQuantification.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 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