Man pages for keyuan/ccube
ccube
| AnnotateCcubeResults | Annotate mydata with Ccube results |
| AnnotateCcubeResults_sv | Annotate mydata with CcubeSV results |
| Assign | Assign data to centers |
| AssignWithCcube | Computing responsibilities (assignment probabilities) with... |
| AssignWithCcube_sv | Computing responsibilities (assignment probabilities) with... |
| bsxfun.se | bsxfun pracma with single expansion (real Matlab style) |
| CcubeCore | Run Ccube Core function |
| ccube_m6 | Run Ccube with model 6: Normal-Binomial. TODO: to be removed... |
| CcubeSVCore | Run Ccube Core function for SV |
| CombineSNVandSVResults | Combine a SNV and a SV result list. |
| cp2ap | Convert ccf to vaf |
| CullEmptyClusters | Remove empty clusters |
| CullEmptyClusters_sv | Remove empty clusters |
| CullSmallClusters | Remove small clusters |
| CullSmallClusters_sv | Remove small clusters |
| GenerateCopyNumberProfile | Simulate a clonal copy number profile |
| GenerateSubClonalCNProfile | Simulate a 2-subclone subclonal copy number profile. |
| GetCcf | Get a rough estimate of ccf and multiplicities |
| GetCcf_sv | Get a rough estimate of ccf and multiplicities |
| GetPurity | Estimate purity |
| GetPurity_sv | Estimate purity |
| gg_color_hue | Ccube color |
| HasClonalCluster | Check if the result has a clonal cluster |
| HasEmptyCluster | Check if the result has empty cluster |
| logsumexp | Compute log(sum(exp(x),dim)) while avoiding numerical... |
| MakeCcubeStdPlot | Make Ccube results plot |
| MakeCcubeStdPlot_sv | Make Ccube results plot |
| MapCcf2VafLinear | Convert ccf to vaf using ccube linear mapping |
| MapVaf2CcfLinear | Convert vaf to ccf using ccube linear mapping |
| MapVaf2CcfPyClone | Convert vaf to ccf using pyclone style mapping |
| MergeClusters | Merge clusters |
| MergeClusters_sv | Merge clusters |
| ParseSnvCnaBattenberg | Parse Battenberg copy number files |
| ParseSnvCnaConsensus | Parse final consensus files |
| ParseSnvCnaOld | Parse old cna_data.txt files |
| ParseSnvCnaPcawg11Format | Parse PCAWG-11 cna format |
| ParseSnvCnaPreConsensus | Parse new consensus files |
| RemoveClusterAndReassignVariants | Remove a (or more) cluster and reassign its data if the... |
| RemoveClusterAndReassignVariants_sv | Remove a (or more) cluster and reassign its data if the... |
| RemoveClusterAndReassignVariantsWithEMsteps | Remove a (or more) cluster and reassign its data if the... |
| RemoveClusterAndReassignVariantsWithEMsteps_sv | Remove a (or more) cluster and reassign its data if the... |
| RemoveClusterAndReassignVariantsWithEstep | Remove a (or more) cluster and reassign its data if the... |
| RemoveClusterAndReassignVariantsWithEstep_sv | Remove a (or more) cluster and reassign its data if the... |
| RunCcubePipeline | Run Ccube analysis |
| RunPostAssignPipeline | A pipeline to post assign events. |
| vbgmm | Variational Bayesian Gaussian mixture model (VB-SMM) |
| vbsmm | Variational Bayesian Student-t mixture model (VB-SMM) |
| WritePcawgFormats | Write files in PCAWG-11 formats, works for both CcubeCore and... |
| WritePcawgFormats_sv | Write files in PCAWG-11 formats, works for both CcubeCore and... |
