Files in pneuvial/c3co
Cancer Cell Clonality using Copy-Number
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/Facetswrapper.R
R/PSCBSwrapper.R
R/alignLoci.R
R/buildSubclones.R
R/c3co.R
R/fitC3co.R
R/get.W.R
R/get.Zt.R
R/getToyData.R
R/heatmap.3.R
R/initializeZt.R
R/mixSubclone.R
R/modelFitStats.R
R/plotFunctions.R
R/positiveFusedLasso.R
R/rSparseWeightMatrix.R
R/segmentData.R
R/utils.R
README.md
appveyor.yml
inst/CanopyComparison/runCanopy.R
inst/Experiments/00.functions.R
inst/Experiments/01.setup.R
inst/Experiments/02.runMethods.R
inst/Experiments/03.plotResults.R
inst/Experiments/README.md
inst/Figures/paperFig.R
inst/GSE47077/R/00.preprocessing.R
inst/GSE47077/R/01.CallGenotypes.R
inst/GSE47077/R/02.TumorBoost.R
inst/GSE47077/R/03.runC3co.R
inst/GSE47077/R/04.figures.R
inst/GSE47077/data/minMaxposByCHR.rds
inst/GSE47077/results_c3co-RK29/featureData,p=2.rds
inst/GSE47077/results_c3co-RK29/featureData,p=3.rds
inst/GSE47077/results_c3co-RK29/featureData,p=4.rds
inst/GSE47077/results_c3co-RK29/featureData,p=5.rds
inst/GSE47077/results_c3co-RK29/featureData,p=6.rds
inst/GSE47077/results_c3co-RK29/featureData,p=7.rds
inst/GSE47077/results_c3co-RK29/featureData,p=8.rds
inst/GSE47077/results_c3co-RK29/segDat.rds
inst/Performance/performance.R
inst/Simu_n=2400/00.functions.R
inst/Simu_n=2400/00.setup.R
inst/Simu_n=2400/01.runMethods.R
inst/Simu_n=2400/02.evalC3co.R
inst/Simu_n=2400/02.evalMethods.R
inst/Simu_n=2400/README.md
inst/Simu_n=24000/00.functions.R
inst/Simu_n=24000/00.setup.R
inst/Simu_n=24000/01.runMethods.R
inst/Simu_n=24000/02.evalMethods.R
inst/WORDLIST
inst/extdata/data4ConsistencyTests.rds
inst/extdata/data_generation.R
inst/testScripts/2019-02_Agro/fitC3co_noiseless.R
inst/testScripts/fitC3co,lowNoise.R
inst/testScripts/fitC3co,noiseless.R
inst/testScripts/postitiveFusedLasso,lowNoise,forceNormal.R
inst/testScripts/postitiveFusedLasso,lowNoise.R
man/FACETSwrapper.Rd
man/PSCBSwrapper.Rd
man/Wplot.Rd
man/Zplot.Rd
man/alignLoci.Rd
man/buildSubclones.Rd
man/c3co.Rd
man/c3coFit-class.Rd
man/createZdf.Rd
man/fitC3co.Rd
man/get.W.Rd
man/get.Zt.Rd
man/getToyData.Rd
man/heatmap.3.Rd
man/initializeZt.Rd
man/loadFACETSdata.Rd
man/loadPSCBSdata.Rd
man/mixSubclones.Rd
man/modelFitStatistics.Rd
man/modelFitStats.Rd
man/nbrOfChromosomes.Rd
man/nbrOfSamples.Rd
man/nbrOfSegments.Rd
man/posFused-class.Rd
man/positiveFusedLasso.Rd
man/pvePlot.Rd
man/pvePlot2.Rd
man/rSpMatrix.Rd
man/rSparseWeightMatrix.Rd
man/sampleNames.Rd
man/segmentData.Rd
man/trackNames.Rd
tests/testthat.R
tests/testthat/test_PSCBS.R
tests/testthat/test_WW.R
tests/testthat/test_buildSubclones.R
tests/testthat/test_c3co.R
tests/testthat/test_consistency_getw.R
tests/testthat/test_consistency_getzt.R
tests/testthat/test_consistency_initializeZt.R
tests/testthat/test_consistency_positiveFusedLasso.R
tests/testthat/test_get.W.R
tests/testthat/test_get.Zt.R
tests/testthat/test_getToyData.R
tests/testthat/test_initializeZt.R
tests/testthat/test_positiveFusedLasso.R
tests/testthat/test_rSparseWeightMatrix.R
vignettes/C3COonSegmentData.Rmd
vignettes/PSCBSwrapper.Rmd
vignettes/c3co-sim-1d.Rmd
vignettes/c3co-sim.Rmd
vignettes/c3co.Rmd
vignettes/c3co.bib
vignettes/img/features.png
vignettes/img/features2.png
vignettes/img/model.png
vignettes/img/model2.png
