Files in steverozen/SynSigGen
Create Catalogs of Synthetic Mutational Spectra
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check-v1.yaml
.github/workflows/check-bioc-3-14.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/AddAllScripts.R
R/CreateAbstract_Nat.R
R/CreateFromReal_Nat.R
R/CreateRandom.R
R/CreateRandomExpKnownSigs.R
R/CreateRandomExpRandomSigs.R
R/CreateRandomExposures.R
R/CreateSynData.R
R/CreateSynSBS1SB5Correlated.R
R/Diff4SynDataSets.R
R/GenerateAndCombineSyntheticTumors.R
R/GenerateListOfSigParams.R
R/GenerateNoisyTumors.R
R/GenerateSyntheticTumors.R
R/GenerateSyntheticTumorsFromSigParams.R
R/MapSPToSASignatureNamesInExposure.R
R/ReadWriteCOMPOSITECatalog.R
R/ReadWriteExposures.R
R/SAAndSPSynDataOneCAType.R
R/SynSigGen.R
R/data.R
R/sysdata.rda
README.Rmd
README.md
SynSigGen.Rproj
data-raw/.gitignore
data-raw/AssessExtracted.R
data-raw/Create.hyper.low.Rmd
data-raw/DirectoryStructureCoordinateTestCatalogs.pptx
data-raw/Laptop.sa.COMPOSITE.exome.subset/Create.SECONDARY.input.R
data-raw/Laptop.sa.COMPOSITE.exome.subset/Split.hyper.vs.non.hyper.R
data-raw/Laptop.sa.COMPOSITE.exome.subset/hyper-pcawg-as-exome-COMPOSITE.csv
data-raw/Laptop.sa.COMPOSITE.exome.subset/non-hyper-pcawg-as-exome-COMPOSITE.csv
data-raw/Laptop.sa.COMPOSITE.exome.subset/pcawg-as-exome-COMPOSITE.csv
data-raw/Laptop.sa.COMPOSITE.exome.subset/sa.COMPOSITE.sigs.csv
data-raw/SA.signatures.random.subsets/10.sigs/ground.truth.syn.catalog.csv
data-raw/SA.signatures.random.subsets/10.sigs/ground.truth.syn.exposures.csv
data-raw/SA.signatures.random.subsets/10.sigs/ground.truth.syn.sigs.csv
data-raw/SA.signatures.random.subsets/15.sigs/ground.truth.syn.catalog.csv
data-raw/SA.signatures.random.subsets/15.sigs/ground.truth.syn.exposures.csv
data-raw/SA.signatures.random.subsets/15.sigs/ground.truth.syn.sigs.csv
data-raw/SA.signatures.random.subsets/25.sigs/ground.truth.syn.catalog.csv
data-raw/SA.signatures.random.subsets/25.sigs/ground.truth.syn.exposures.csv
data-raw/SA.signatures.random.subsets/25.sigs/ground.truth.syn.sigs.csv
data-raw/SA.signatures.random.subsets/3.sigs/ground.truth.syn.catalog.csv
data-raw/SA.signatures.random.subsets/3.sigs/ground.truth.syn.exposures.csv
data-raw/SA.signatures.random.subsets/3.sigs/ground.truth.syn.sigs.csv
data-raw/SA.signatures.random.subsets/5.sigs/ground.truth.syn.catalog.csv
data-raw/SA.signatures.random.subsets/5.sigs/ground.truth.syn.exposures.csv
data-raw/SA.signatures.random.subsets/5.sigs/ground.truth.syn.sigs.csv
data-raw/SA.signatures.random.subsets/log.txt
data-raw/SBS1SBS5parameter.csv
data-raw/SP.signatures.random.subsets/10.sigs/ground.truth.syn.catalog.csv
data-raw/SP.signatures.random.subsets/10.sigs/ground.truth.syn.exposures.csv
data-raw/SP.signatures.random.subsets/10.sigs/ground.truth.syn.sigs.csv
data-raw/SP.signatures.random.subsets/15.sigs/ground.truth.syn.catalog.csv
data-raw/SP.signatures.random.subsets/15.sigs/ground.truth.syn.exposures.csv
data-raw/SP.signatures.random.subsets/15.sigs/ground.truth.syn.sigs.csv
data-raw/SP.signatures.random.subsets/25.sigs/ground.truth.syn.catalog.csv
data-raw/SP.signatures.random.subsets/25.sigs/ground.truth.syn.exposures.csv
data-raw/SP.signatures.random.subsets/25.sigs/ground.truth.syn.sigs.csv
data-raw/SP.signatures.random.subsets/3.sigs/ground.truth.syn.catalog.csv
data-raw/SP.signatures.random.subsets/3.sigs/ground.truth.syn.exposures.csv
data-raw/SP.signatures.random.subsets/3.sigs/ground.truth.syn.sigs.csv
data-raw/SP.signatures.random.subsets/5.sigs/ground.truth.syn.catalog.csv
data-raw/SP.signatures.random.subsets/5.sigs/ground.truth.syn.exposures.csv
data-raw/SP.signatures.random.subsets/5.sigs/ground.truth.syn.sigs.csv
data-raw/SP.signatures.random.subsets/log.txt
data-raw/SynSigGen_1.1.1.pdf
data-raw/compare.SP.and.SA.sigs/COSMICv2.pdf
data-raw/compare.SP.and.SA.sigs/COSMICv3.vs.v2.csv
data-raw/compare.SP.and.SA.sigs/COSMICv3.vs.v2.xlsx
data-raw/compare.SP.and.SA.sigs/SA.to.SP.csv
data-raw/compare.SP.and.SA.sigs/SA.to.SP.pdf
data-raw/compare.SP.and.SA.sigs/SA.to.SP.xlsx
data-raw/compare.SP.and.SA.sigs/SP.to.SA.csv
data-raw/compare.SP.and.SA.sigs/SP.to.SA.pdf
data-raw/compare.SP.and.SA.sigs/SP.to.SA.xlsx
data-raw/compare.SP.and.SA.sigs/compare.SP.and.SA.SBS96.R
data-raw/compare.SP.and.SA.sigs/other.info.txt
data-raw/diff.check.syn.hyper.txt
data-raw/exome-versions-of-pcawg/README-2018-12-04.txt
data-raw/exome-versions-of-pcawg/pcawg-as-exome-1536.csv
data-raw/exome-versions-of-pcawg/pcawg-as-exome-192.csv
data-raw/exome-versions-of-pcawg/pcawg-as-exome-96.csv
data-raw/for.generating.package.data/PCAWG_sigProfiler_SBS_signatures_in_samples.csv
data-raw/for.generating.package.data/SignatureAnalyzer_COMPOSITE_DBS.signature.042018.txt
data-raw/for.generating.package.data/SignatureAnalyzer_COMPOSITE_ID.signature.031918.txt
data-raw/for.generating.package.data/SignatureAnalyzer_COMPOSITE_SBS_W1536.signature.031918.txt
data-raw/for.generating.package.data/SignatureAnalyzer_COMPOSITE_SBS_W96.signature.031918.txt
data-raw/for.generating.package.data/SignatureAnalyzer_COMPOSITE_SNV.activity.FULL_SET.031918.txt
data-raw/for.generating.package.data/SignatureAnalyzer_COMPOSITE_SNV.activity.no_POLE_MSI_SKIN_TMZ.031918.txt
data-raw/for.generating.package.data/SignatureAnalyzer_DBS.signature.20180420.txt
data-raw/for.generating.package.data/SignatureAnalyzer_ID.signature.012718.txt
data-raw/for.generating.package.data/get.SA.and.SP.real.exposures.R
data-raw/for.generating.package.data/get.SA.signatures.R
data-raw/for.generating.package.data/get.SP.signatures.R
data-raw/for.generating.package.data/get.signature.params.R
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.abst/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.Bladder-TCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.Bladder-TCC.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.Bladder-TCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.Skin-Melanoma.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.Skin-Melanoma.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.Skin-Melanoma.real.input.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.Bladder-TCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.Bladder-TCC.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.Bladder-TCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.Skin-Melanoma.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.Skin-Melanoma.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.Skin-Melanoma.real.input.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.abst/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.Kidney-RCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.Kidney-RCC.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.Kidney-RCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.Ovary-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.Ovary-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.Ovary-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.Kidney-RCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.Kidney-RCC.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.Kidney-RCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.Ovary-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.Ovary-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.Ovary-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.30.random.sigs/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sa.HYPER.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sa.HYPER.parms.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sa.HYPER.real.input.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sa.NO.HYPER.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sa.NO.HYPER.parms.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sa.NO.HYPER.real.input.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sp.HYPER.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sp.HYPER.parms.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sp.HYPER.real.input.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sp.NO.HYPER.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sp.NO.HYPER.parms.csv
data-raw/long.test.regression.data/syn.hyper.low.START/sp.NO.HYPER.real.input.exposure.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.primary/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sa.secondary/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sp/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sp/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sp/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.hyper.low.sp/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.hyper.low.sp/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.hyper.low.sp/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.many.types/sa.Bladder-TCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Bladder-TCC.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Bladder-TCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Bone-Osteosarc.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Bone-Osteosarc.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Bone-Osteosarc.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Breast-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Breast-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Breast-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Cervix-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Cervix-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Cervix-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Eso-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Eso-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Eso-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Kidney-RCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Kidney-RCC.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Kidney-RCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Lung-SCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Lung-SCC.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Lung-SCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Ovary-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Ovary-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Ovary-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Stomach-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.Stomach-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sa.Stomach-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.many.types/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.many.types/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.many.types/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.many.types/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.many.types/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.many.types/sp.Bladder-TCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Bladder-TCC.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Bladder-TCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Bone-Osteosarc.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Bone-Osteosarc.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Bone-Osteosarc.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Breast-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Breast-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Breast-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Cervix-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Cervix-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Cervix-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Eso-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Eso-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Eso-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Kidney-RCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Kidney-RCC.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Kidney-RCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Lung-SCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Lung-SCC.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Lung-SCC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Ovary-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Ovary-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Ovary-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Stomach-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.Stomach-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.many.types/sp.Stomach-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.exposure.csv
data-raw/long.test.regression.data/syn.many.types/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.many.types/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.many.types/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.many.types/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.many.types/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.many.types/sp.sp/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.pancreas/sa.Panc-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sa.Panc-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.pancreas/sa.Panc-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sa.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.96/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.96/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.96/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.pancreas/sp.Panc-AdenoCA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sp.Panc-AdenoCA.parms.csv
data-raw/long.test.regression.data/syn.pancreas/sp.Panc-AdenoCA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sp.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sp/ground.truth.syn.catalog.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sp/ground.truth.syn.exposures.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sp/ground.truth.syn.sigs.csv
data-raw/sa.COMPOSITE.exome.subset/Create.SECONDARY.input.R
data-raw/sa.COMPOSITE.exome.subset/Split.hyper.vs.non.hyper.R
data-raw/sa.COMPOSITE.exome.subset/hyper-pcawg-as-exome-COMPOSITE.csv
data-raw/sa.COMPOSITE.exome.subset/non-hyper-pcawg-as-exome-COMPOSITE.csv
data-raw/sa.COMPOSITE.exome.subset/pcawg-as-exome-COMPOSITE.csv
data-raw/sa.COMPOSITE.exome.subset/sa.COMPOSITE.sigs.csv
data-raw/sa.DBS.exome.subset/pcawg-as-exome-DBS.csv
data-raw/sa.DBS.exome.subset/sa.DBS.sigs.csv
data-raw/sa.ID.exome.subset/pcawg-as-exome-ID.csv
data-raw/sa.ID.exome.subset/sa.ID.sigs.csv
data-raw/todo.txt
data/SBS1SBS5datasetNames.rda
data/SBS1SBS5parameter.rda
data/sa.96.sigs.rda
data/sa.COMPOSITE.sigs.rda
data/sa.DBS.sigs.rda
data/sa.ID.sigs.rda
data/sa.all.real.exposures.rda
data/sa.no.hyper.real.exposures.rda
data/signature.params.rda
data/sp.all.real.exposures.rda
data/sp.no.hyper.real.exposures.rda
data/sp.sigs.rda
inst/WORDLIST
man/AddAllScripts.Rd
man/AddNoise.Rd
man/AddScript.Rd
man/AssignPresentAbsentOneSample.Rd
man/BladderSkin1000.Rd
man/Create.2.7a.7b.Abstract.Rd
man/Create.3.5.40.Abstract.Rd
man/Create1CatRandomExpRandomSigs.Rd
man/CreateAndWriteCatalog.Rd
man/CreateFromReal.Rd
man/CreateMeanAndStdevForSigs.Rd
man/CreateMixedTumorTypeSyntheticData.Rd
man/CreateNumSigsPerTumor.Rd
man/CreateOnePairOfRandomCatalogs.Rd
man/CreateOneRandomMutSigProfile.Rd
man/CreateRandomExposures.Rd
man/CreateRandomMutSigProfiles.Rd
man/CreateRandomSAAndSPSynCatalogs.Rd
man/CreateRandomSyn.Rd
man/CreateSBS1SBS5CorrelatedSyntheticData.Rd
man/CreateSBS1SBS5CorrelatedSyntheticDataOneDataset.Rd
man/CreateSynCatalogs.Rd
man/Diff4SynDataSets.Rd
man/ExposureNums2Exposures.Rd
man/GenSBS1SBS5Exposure.Rd
man/GenSBS1SBS5ExposureOneTumor.Rd
man/GenerateAllRandomSA.Rd
man/GenerateAllRandomSP.Rd
man/GenerateListOfSigParams.Rd
man/GenerateNoisyTumors.Rd
man/GenerateSynAbstract.Rd
man/GenerateSynExposureOneSample.Rd
man/GenerateSynFromReal.Rd
man/GenerateSyntheticExposures.Rd
man/GenerateSyntheticTumors.Rd
man/GenerateSyntheticTumorsFromSigParams.Rd
man/GetSynSigParamsFromExposures.Rd
man/ManyTypes2700.Rd
man/MapSPToSASignatureNamesInExposure.Rd
man/Merge2Exposures.Rd
man/MergeExposures.Rd
man/MutationalSignatures.Rd
man/NewCreateAndWriteCatalog.Rd
man/NewDiff4SynDataSets.Rd
man/OLD.SplitCatCOMPOSITE.Rd
man/OutDir.Rd
man/PancAdenoCA1000.Rd
man/ParametersSALike.Rd
man/ParametersSPLike.Rd
man/PlotCorrelationScatterplot.Rd
man/PlotCorrelationScatterplotForExposures.Rd
man/RCCOvary1000.Rd
man/ReadCatCOMPOSITE.Rd
man/ReadExposure.Rd
man/ReadSynapseExposure.Rd
man/RealExposures.Rd
man/SAAndSPSynDataOneCAType.Rd
man/SBS1SBS5datasetNames.Rd
man/SBS1SBS5parameter.Rd
man/SynSigGen.Rd
man/SynSigParamsOneSignature.Rd
man/WriteCatCOMPOSITE.Rd
man/WriteExposure.Rd
man/WriteSynSigParams.Rd
man/present.sigs.Rd
man/signature.params.Rd
man/xFixSASigNames.Rd
tests/testthat.R
tests/testthat/Bladder-Melanoma-test/sa.Bladder-TCC.generic.syn.exposure.csv
tests/testthat/Bladder-Melanoma-test/sa.Bladder-TCC.parms.csv
tests/testthat/Bladder-Melanoma-test/sa.Bladder-TCC.real.input.exposure.csv
tests/testthat/Bladder-Melanoma-test/sa.Skin-Melanoma.generic.syn.exposure.csv
tests/testthat/Bladder-Melanoma-test/sa.Skin-Melanoma.parms.csv
tests/testthat/Bladder-Melanoma-test/sa.Skin-Melanoma.real.input.exposure.csv
tests/testthat/Bladder-Melanoma-test/sa.exposure.csv
tests/testthat/Bladder-Melanoma-test/sp.Bladder-TCC.generic.syn.exposure.csv
tests/testthat/Bladder-Melanoma-test/sp.Bladder-TCC.parms.csv
tests/testthat/Bladder-Melanoma-test/sp.Bladder-TCC.real.input.exposure.csv
tests/testthat/Bladder-Melanoma-test/sp.Skin-Melanoma.generic.syn.exposure.csv
tests/testthat/Bladder-Melanoma-test/sp.Skin-Melanoma.parms.csv
tests/testthat/Bladder-Melanoma-test/sp.Skin-Melanoma.real.input.exposure.csv
tests/testthat/Bladder-Melanoma-test/sp.exposure.csv
tests/testthat/SignatureAnalyzer4MatchedCatalogs.out.Rdata
tests/testthat/mixed.types.Rdata
tests/testthat/rand.syn.96.sigs.Rdata
tests/testthat/rdata/Panc-AdenoCA.123/sa.Panc-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.Panc-AdenoCA.parms.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.Panc-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.exposure.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/Panc-AdenoCA.123/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.Panc-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.Panc-AdenoCA.parms.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.Panc-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.exposure.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/rdata/Panc-AdenoCA.123/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.1/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.1/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.1/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.2/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.2/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.2/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.3/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.3/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.3/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.6/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.6/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.1.Rsq.0.6/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.1/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.1/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.1/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.2/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.2/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.2/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.3/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.3/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.3/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.6/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.6/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.0.5.Rsq.0.6/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.1/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.1/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.1/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.2/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.2/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.2/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.3/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.3/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.3/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.6/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.6/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.1.Rsq.0.6/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.1/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.1/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.1/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.2/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.2/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.2/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.3/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.3/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.3/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.6/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.6/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.10.Rsq.0.6/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.1/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.1/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.1/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.2/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.2/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.2/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.3/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.3/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.3/ground.truth.syn.sigs.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.6/ground.truth.syn.catalog.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.6/ground.truth.syn.exposures.csv
tests/testthat/rdata/SBS1.5/S.2.Rsq.0.6/ground.truth.syn.sigs.csv
tests/testthat/rdata/abst.2.7a.7b/sa.generic.syn.exposure.csv
tests/testthat/rdata/abst.2.7a.7b/sa.parms.csv
tests/testthat/rdata/abst.2.7a.7b/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/rdata/abst.2.7a.7b/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/rdata/abst.2.7a.7b/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/rdata/abst.2.7a.7b/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/abst.2.7a.7b/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/abst.2.7a.7b/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/abst.2.7a.7b/sp.generic.syn.exposure.csv
tests/testthat/rdata/abst.2.7a.7b/sp.parms.csv
tests/testthat/rdata/abst.2.7a.7b/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/abst.2.7a.7b/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/abst.2.7a.7b/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/abst.2.7a.7b/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/rdata/abst.2.7a.7b/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/rdata/abst.2.7a.7b/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/rdata/many.syn.191906/sa.Bladder-TCC.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Bladder-TCC.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Bladder-TCC.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Bone-Osteosarc.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Bone-Osteosarc.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Bone-Osteosarc.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Breast-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Breast-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Breast-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Cervix-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Cervix-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Cervix-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Eso-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Eso-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Eso-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Kidney-RCC.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Kidney-RCC.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Kidney-RCC.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Lung-SCC.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Lung-SCC.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Lung-SCC.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Ovary-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Ovary-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Ovary-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Stomach-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.Stomach-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sa.Stomach-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.exposure.csv
tests/testthat/rdata/many.syn.191906/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/rdata/many.syn.191906/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/rdata/many.syn.191906/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/rdata/many.syn.191906/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/many.syn.191906/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/many.syn.191906/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/many.syn.191906/sp.Bladder-TCC.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Bladder-TCC.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Bladder-TCC.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Bone-Osteosarc.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Bone-Osteosarc.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Bone-Osteosarc.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Breast-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Breast-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Breast-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Cervix-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Cervix-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Cervix-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Eso-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Eso-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Eso-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Kidney-RCC.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Kidney-RCC.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Kidney-RCC.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Lung-SCC.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Lung-SCC.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Lung-SCC.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Ovary-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Ovary-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Ovary-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Stomach-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.Stomach-AdenoCA.parms.csv
tests/testthat/rdata/many.syn.191906/sp.Stomach-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.exposure.csv
tests/testthat/rdata/many.syn.191906/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/many.syn.191906/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/many.syn.191906/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/many.syn.191906/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/rdata/many.syn.191906/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/rdata/many.syn.191906/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.k.sigs/summary.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.10.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.10.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.10.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.15.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.15.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.15.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.25.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.25.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.25.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.3.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.3.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.3.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.5.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.5.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.k.sigs/syn.data.5.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.r.sigs/summary.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.10.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.10.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.10.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.15.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.15.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.15.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.25.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.25.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.25.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.3.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.3.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.3.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.5.sigs/ground.truth.syn.catalog.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.5.sigs/ground.truth.syn.exposures.csv
tests/testthat/rdata/r.exp.r.sigs/syn.data.5.sigs/ground.truth.syn.sigs.csv
tests/testthat/rdata/random.5/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/rdata/random.5/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/rdata/random.5/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/rdata/random.5/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/random.5/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/random.5/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/random.5/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/random.5/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/random.5/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/random.5/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/rdata/random.5/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/rdata/random.5/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/rdata/rcc.etc/sa.Kidney-RCC.generic.syn.exposure.csv
tests/testthat/rdata/rcc.etc/sa.Kidney-RCC.parms.csv
tests/testthat/rdata/rcc.etc/sa.Kidney-RCC.real.input.exposure.csv
tests/testthat/rdata/rcc.etc/sa.Ovary-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/rcc.etc/sa.Ovary-AdenoCA.parms.csv
tests/testthat/rdata/rcc.etc/sa.Ovary-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/rcc.etc/sa.exposure.csv
tests/testthat/rdata/rcc.etc/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/rdata/rcc.etc/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/rdata/rcc.etc/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/rdata/rcc.etc/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/rcc.etc/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/rcc.etc/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/rcc.etc/sp.Kidney-RCC.generic.syn.exposure.csv
tests/testthat/rdata/rcc.etc/sp.Kidney-RCC.parms.csv
tests/testthat/rdata/rcc.etc/sp.Kidney-RCC.real.input.exposure.csv
tests/testthat/rdata/rcc.etc/sp.Ovary-AdenoCA.generic.syn.exposure.csv
tests/testthat/rdata/rcc.etc/sp.Ovary-AdenoCA.parms.csv
tests/testthat/rdata/rcc.etc/sp.Ovary-AdenoCA.real.input.exposure.csv
tests/testthat/rdata/rcc.etc/sp.exposure.csv
tests/testthat/rdata/rcc.etc/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/rcc.etc/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/rcc.etc/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/rcc.etc/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/rdata/rcc.etc/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/rdata/rcc.etc/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/rdata/syn.30.random.sigs/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/rdata/syn.30.random.sigs/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/rdata/syn.30.random.sigs/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/rdata/syn.30.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/syn.30.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/syn.30.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/syn.30.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/rdata/syn.30.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/rdata/syn.30.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/rdata/syn.30.random.sigs/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/rdata/syn.30.random.sigs/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/rdata/syn.30.random.sigs/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/sa.COMP.exome.test.input/Create.SECONDARY.input.R
tests/testthat/sa.COMP.exome.test.input/hyper-pcawg-as-exome-COMPOSITE.csv
tests/testthat/sa.COMP.exome.test.input/non-hyper-pcawg-as-exome-COMPOSITE.csv
tests/testthat/sa.COMP.exome.test.input/pcawg-as-exome-COMPOSITE.csv
tests/testthat/sa.COMP.exome.test.input/sa.COMPOSITE.sigs.csv
tests/testthat/sa.test.param.delta.Rdata
tests/testthat/sa.test.param.in.Rdata
tests/testthat/sa.test.param.out.Rdata
tests/testthat/sa.test.synthetic.exposures.Rdata
tests/testthat/signature.analyzer.sa.sa.96.out.Rdata
tests/testthat/signature.analyzer.sa.sa.COMPOSITE.out
tests/testthat/test-AddNoise.R
tests/testthat/test-CreateFromReal.R
tests/testthat/test-CreateRandExpKnownSigs.R
tests/testthat/test-CreateRandExpRandSigs.R
tests/testthat/test-CreateSBS1SBS5.R
tests/testthat/test-GenerateSyntheticTumors.R
tests/testthat/test-GenerateSyntheticTumorsFromSigParams.R
tests/testthat/test-IDSigs.R
tests/testthat/test-ReadWriteExposure.R
tests/testthat/test-random.sigs.R
tests/testthat/test.CreateAbstract.R
tests/testthat/test.get.synsig.params.R
tests/testthat/test.random.sigs/sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/test.random.sigs/sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/test.random.sigs/sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/test.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/test.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/test.random.sigs/sa.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/test.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/test.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/test.random.sigs/sp.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/test.random.sigs/sp.sp/ground.truth.syn.catalog.csv
tests/testthat/test.random.sigs/sp.sp/ground.truth.syn.exposures.csv
tests/testthat/test.random.sigs/sp.sp/ground.truth.syn.sigs.csv
tests/testthat/testdata/AddNoise.test.results.Rdata
tests/testthat/testdata/CreateRandomSyn.retval.Rdata
tests/testthat/testdata/ID.test.results.Rdata
tests/testthat/testdata/PancAdenoCA1000.retval.Rdata
tests/testthat/testdata/tiny.exposure.csv
tests/testthat/testdata/tiny.exposure.dup.csv
tests/testthat/xtest-random.sigs.R
