Files in keyuan/ccube

ccube

R/ccube.R R/ccube_sv.R R/util.R R/vbgmm.R R/vbsmm.R R/wrapper.R README.md inst/test_life_history_data.R inst/test_marek_mixture.R inst/test_pcawg_consensus_non_integer_cn.R inst/test_pcawg_sv.R inst/test_pcawg_sv_for_geoff.R inst/test_pcawg_sv_single_sample.R inst/test_pcawg_sv_single_sample_1.R inst/test_post_assign_snv.R inst/test_post_assign_sv.R inst/test_qc_fix.R inst/test_subclonal_cn_snv.R inst/test_subclonal_cn_snv_consensus_copy_number.R inst/test_subclonal_cn_sv.R inst/test_subclonal_cn_sv_consensus_format.R inst/test_sv.R man/AnnotateCcubeResults.Rd man/AnnotateCcubeResults_sv.Rd man/Assign.Rd man/AssignWithCcube.Rd man/AssignWithCcube_sv.Rd man/CcubeCore.Rd man/CcubeSVCore.Rd man/CombineSNVandSVResults.Rd man/CullEmptyClusters.Rd man/CullEmptyClusters_sv.Rd man/CullSmallClusters.Rd man/CullSmallClusters_sv.Rd man/GenerateCopyNumberProfile.Rd man/GenerateSubClonalCNProfile.Rd man/GetCcf.Rd man/GetCcf_sv.Rd man/GetPurity.Rd man/GetPurity_sv.Rd man/HasClonalCluster.Rd man/HasEmptyCluster.Rd man/MakeCcubeStdPlot.Rd man/MakeCcubeStdPlot_sv.Rd man/MapCcf2VafLinear.Rd man/MapVaf2CcfLinear.Rd man/MapVaf2CcfPyClone.Rd man/MergeClusters.Rd man/MergeClusters_sv.Rd man/ParseSnvCnaBattenberg.Rd man/ParseSnvCnaConsensus.Rd man/ParseSnvCnaOld.Rd man/ParseSnvCnaPcawg11Format.Rd man/ParseSnvCnaPreConsensus.Rd man/RemoveClusterAndReassignVariants.Rd man/RemoveClusterAndReassignVariantsWithEMsteps.Rd man/RemoveClusterAndReassignVariantsWithEMsteps_sv.Rd man/RemoveClusterAndReassignVariantsWithEstep.Rd man/RemoveClusterAndReassignVariantsWithEstep_sv.Rd man/RemoveClusterAndReassignVariants_sv.Rd man/RunCcubePipeline.Rd man/RunPostAssignPipeline.Rd man/WritePcawgFormats.Rd man/WritePcawgFormats_sv.Rd man/bsxfun.se.Rd man/ccube_m6.Rd man/cp2ap.Rd man/gg_color_hue.Rd man/logsumexp.Rd man/vbgmm.Rd man/vbsmm.Rd vignettes/ccube.Rmd