Files in WuyangFF95/SynSigEval
Evaluate Results of Mutational Signature Analysis Software on Synthetic Spectra Created by Package SynSigGen
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/BestSignatureAnalyzerResult.R
R/EMuinteraction.R
R/MultiModalMuSigInteraction.R
R/PlotCOMPOSITECatalogs.R
R/ReadAndAnalyzeExposures.R
R/ReadAndAnalyzeSigs.R
R/RelabelExSigs.R
R/SigProfilerInteraction.R
R/SplitCatCOMPOSITE.R
R/SummarizeMultiRuns.R
R/SummarizeMultiToolsMultiDatasets.R
R/SummarizeMultiToolsMultiDatasetsAttr.R
R/SummarizeMultiToolsMultiDatasetsExtr.R
R/SummarizeOneToolMultiDatasets.R
R/SummarizeResultsOneExtrAttrSubdir.R
R/SummarizeResultsSA.R
R/SummarizeResultsSP.R
R/SummarizeResultshelmsman.R
R/SummarizeSigOneAttrSubdir.R
R/SummarizeSigOneSubdir.R
R/SynSigEval.R
R/data.R
R/helmsmanInteraction.R
README.Rmd
README.md
SynSigEval.Rproj
data-raw/.gitignore
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/SynSigEval_0.4.0.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/deprecated.codes/SummarizeMultiToolsOneDataset.R
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/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.96/1.run.SA.R
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/3.run.SA.R
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/4.run.SA.R
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/2.run.SA.R
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.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.BLADDER.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.BLADDER.real.input.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.SKIN.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.SKIN.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sa.SKIN.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.96/1.run.SA.R
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/3.run.SA.R
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.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.BLADDER.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.BLADDER.real.input.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.SKIN.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.SKIN.parms.csv
data-raw/long.test.regression.data/syn.2.7a.7b.bladder.and.melanoma/sp.SKIN.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/4.run.SA.R
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/2.run.SA.R
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.OVA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.OVA.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.OVA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.RCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.RCC.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sa.RCC.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.OVA.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.OVA.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.OVA.real.input.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.RCC.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.RCC.parms.csv
data-raw/long.test.regression.data/syn.3.5.40.rcc.and.ovary/sp.RCC.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.96/1.run.SA.R
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/3.run.SA.R
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/4.run.SA.R
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/2.run.SA.R
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.96/1.run.SA.R
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/3.run.SA.R
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/4.run.SA.R
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/2.run.SA.R
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.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sa.PANC.parms.csv
data-raw/long.test.regression.data/syn.pancreas/sa.PANC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sa.parms.csv
data-raw/long.test.regression.data/syn.pancreas/sa.sa.96/1.run.SA.R
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/3.run.SA.R
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.generic.syn.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sp.PANC.parms.csv
data-raw/long.test.regression.data/syn.pancreas/sp.PANC.real.input.exposure.csv
data-raw/long.test.regression.data/syn.pancreas/sp.parms.csv
data-raw/long.test.regression.data/syn.pancreas/sp.sa.COMPOSITE/4.run.SA.R
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/2.run.SA.R
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
inst/WORDLIST
man/BestSignatureAnalyzerResult.Rd
man/CopyBestSignatureAnalyzerResult.Rd
man/CreateEMuOutput.Rd
man/CreateMultiModalMuSigOutput.Rd
man/CreatehelmsmanOutput.Rd
man/ICAMSCatalog2EMu.Rd
man/ICAMSCatalog2MM.Rd
man/ICAMSCatalog2helmsman.Rd
man/MMCatalog2ICAMS.Rd
man/Plot96PartOfComposite.Rd
man/PlotCatCOMPOSITE.Rd
man/ReadAndAnalyzeExposures.Rd
man/ReadAndAnalyzeSigs.Rd
man/ReadEMuCatalog.Rd
man/ReadEMuExposureFile.Rd
man/ReadExposureMM.Rd
man/ReadSigProfilerExposure.Rd
man/ReadhelmsmanExposure.Rd
man/RelabelExSigs.Rd
man/SignatureAnalyzerSummarizeSBS1SBS5.Rd
man/SignatureAnalyzerSummarizeTopLevel.Rd
man/SplitCatCOMPOSITE.Rd
man/SummarizeMultiRuns.Rd
man/SummarizeMultiToolsMultiDatasets.Rd
man/SummarizeMultiToolsMultiDatasetsAttr.Rd
man/SummarizeMultiToolsMultiDatasetsExtr.Rd
man/SummarizeOneToolMultiDatasets.Rd
man/SummarizeSigOneAttrSubdir.Rd
man/SummarizeSigOneExtrAttrSubdir.Rd
man/SummarizeSigOneSASubdir.Rd
man/SummarizeSigOneSigProExtractorSubdir.Rd
man/SummarizeSigOneSigProSSSubdir.Rd
man/SummarizeSigOneSubdir.Rd
man/SummarizeSigOnehelmsmanSubdir.Rd
man/SummarizeSigProExtractor.Rd
man/SynSigEval.Rd
man/helmsmanCatalog2ICAMS.Rd
tests/SBS96.ground.truth/JOB_METADATA.txt
tests/SBS96.ground.truth/ground.truth.syn.catalog.csv
tests/SBS96.ground.truth/ground.truth.syn.exposures.csv
tests/SBS96.ground.truth/ground.truth.syn.sigs.csv
tests/SBS96/All_solutions_stat.csv
tests/SBS96/SBS96_selection_plot.pdf
tests/SBS96/Samples.txt
tests/SBS96/Suggested_Solution/De_Novo_Solution/.gitignore
tests/SBS96/Suggested_Solution/De_Novo_Solution/De_Novo_Solution_Activities_SBS96.txt
tests/SBS96/Suggested_Solution/De_Novo_Solution/De_Novo_Solution_Signatures_SBS96.txt
tests/extracted.signatures.csv
tests/inferred.exposures.csv
tests/testthat.R
tests/testthat/SigProExtractor.sp.SBS96.out.Rdata
tests/testthat/SignatureAnalyzer.sa.sa.96.out.Rdata
tests/testthat/SignatureAnalyzer.sa.sa.COMPOSITE.out.RData
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.COMP.exome.test.ref.output/Create.SECONDARY.input.R
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/best.run/info.txt
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/best.run/sa.output.other.data.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/best.run/sa.output.raw.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/best.run/sa.output.sigs.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.1/sa.output.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.1/sa.output.other.data.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.1/sa.output.raw.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.1/sa.output.sigs.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.2/sa.output.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.2/sa.output.other.data.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.2/sa.output.raw.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/PRIMARY/sa.run.2/sa.output.sigs.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY.catalog.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.1/sa.output.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.1/sa.output.other.data.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.1/sa.output.raw.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.1/sa.output.sigs.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.2/sa.output.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.2/sa.output.other.data.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.2/sa.output.raw.exp.csv
tests/testthat/sa.COMP.exome.test.ref.output/SECONDARY/sa.run.2/sa.output.sigs.csv
tests/testthat/sa.COMP.exome.test.ref.output/Split.hyper.vs.non.hyper.R
tests/testthat/sa.COMP.exome.test.ref.output/hyper-pcawg-as-exome-COMPOSITE.csv
tests/testthat/sa.COMP.exome.test.ref.output/non-hyper-pcawg-as-exome-COMPOSITE.csv
tests/testthat/sa.COMP.exome.test.ref.output/pcawg-as-exome-COMPOSITE.csv
tests/testthat/sa.COMP.exome.test.ref.output/sa.COMPOSITE.sigs.csv
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/test.sa.COMPOSITE/.gitignore
tests/testthat/test.sa.COMPOSITE/ground.truth.syn.catalog.csv
tests/testthat/test.sa.COMPOSITE/ground.truth.syn.exposures.csv
tests/testthat/test.sa.COMPOSITE/ground.truth.syn.sigs.csv
tests/testthat/test.sa.COMPOSITE/sa.results/1.run/sa.output.exp.csv
tests/testthat/test.sa.COMPOSITE/sa.results/1.run/sa.output.other.data.csv
tests/testthat/test.sa.COMPOSITE/sa.results/1.run/sa.output.sigs.csv
tests/testthat/test.sa.getbest.R
tests/testthat/test.sa.results1/sa.run.10/sa.output.other.data.csv
tests/testthat/test.sa.results1/sa.run.11/sa.output.other.data.csv
tests/testthat/test.sa.results1/sa.run.12/sa.output.exp.csv
tests/testthat/test.sa.results1/sa.run.12/sa.output.other.data.csv
tests/testthat/test.sa.results1/sa.run.12/sa.output.raw.exp.csv
tests/testthat/test.sa.results1/sa.run.12/sa.output.sigs.csv
tests/testthat/test.sa.results1/sa.run.13/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.1/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.10/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.11/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.12/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.13/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.14/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.15/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.16/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.17/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.18/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.19/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.2/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.20/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.3/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.4/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.5/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.6/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.7/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.8/sa.output.other.data.csv
tests/testthat/test.sa.results2/sa.run.9/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.1/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.10/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.11/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.12/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.13/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.14/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.15/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.16/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.17/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.18/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.19/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.2/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.20/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.3/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.4/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.5/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.6/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.7/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.8/sa.output.other.data.csv
tests/testthat/test.sa.results3/sa.run.9/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.1/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.10/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.11/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.12/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.13/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.14/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.15/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.16/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.17/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.18/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.19/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.2/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.20/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.3/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.4/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.5/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.6/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.7/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.8/sa.output.other.data.csv
tests/testthat/test.sa.results4/sa.run.9/sa.output.other.data.csv
tests/testthat/test.sa.sa.96/ground.truth.syn.catalog.csv
tests/testthat/test.sa.sa.96/ground.truth.syn.exposures.csv
tests/testthat/test.sa.sa.96/ground.truth.syn.sigs.csv
tests/testthat/test.sa.sa.96/sa.results/1.run.sa.sa.96/sa.output.exp.csv
tests/testthat/test.sa.sa.96/sa.results/1.run.sa.sa.96/sa.output.other.data.csv
tests/testthat/test.sa.sa.96/sa.results/1.run.sa.sa.96/sa.output.sigs.csv
tests/testthat/test.summarize.one.dir.R
