Man pages for keyuan/ccube
ccube

AnnotateCcubeResultsAnnotate mydata with Ccube results
AnnotateCcubeResults_svAnnotate mydata with CcubeSV results
AssignAssign data to centers
AssignWithCcubeComputing responsibilities (assignment probabilities) with...
AssignWithCcube_svComputing responsibilities (assignment probabilities) with...
bsxfun.sebsxfun pracma with single expansion (real Matlab style)
CcubeCoreRun Ccube Core function
ccube_m6Run Ccube with model 6: Normal-Binomial. TODO: to be removed...
CcubeSVCoreRun Ccube Core function for SV
CombineSNVandSVResultsCombine a SNV and a SV result list.
cp2apConvert ccf to vaf
CullEmptyClustersRemove empty clusters
CullEmptyClusters_svRemove empty clusters
CullSmallClustersRemove small clusters
CullSmallClusters_svRemove small clusters
GenerateCopyNumberProfileSimulate a clonal copy number profile
GenerateSubClonalCNProfileSimulate a 2-subclone subclonal copy number profile.
GetCcfGet a rough estimate of ccf and multiplicities
GetCcf_svGet a rough estimate of ccf and multiplicities
GetPurityEstimate purity
GetPurity_svEstimate purity
gg_color_hueCcube color
HasClonalClusterCheck if the result has a clonal cluster
HasEmptyClusterCheck if the result has empty cluster
logsumexpCompute log(sum(exp(x),dim)) while avoiding numerical...
MakeCcubeStdPlotMake Ccube results plot
MakeCcubeStdPlot_svMake Ccube results plot
MapCcf2VafLinearConvert ccf to vaf using ccube linear mapping
MapVaf2CcfLinearConvert vaf to ccf using ccube linear mapping
MapVaf2CcfPyCloneConvert vaf to ccf using pyclone style mapping
MergeClustersMerge clusters
MergeClusters_svMerge clusters
ParseSnvCnaBattenbergParse Battenberg copy number files
ParseSnvCnaConsensusParse final consensus files
ParseSnvCnaOldParse old cna_data.txt files
ParseSnvCnaPcawg11FormatParse PCAWG-11 cna format
ParseSnvCnaPreConsensusParse new consensus files
RemoveClusterAndReassignVariantsRemove a (or more) cluster and reassign its data if the...
RemoveClusterAndReassignVariants_svRemove a (or more) cluster and reassign its data if the...
RemoveClusterAndReassignVariantsWithEMstepsRemove a (or more) cluster and reassign its data if the...
RemoveClusterAndReassignVariantsWithEMsteps_svRemove a (or more) cluster and reassign its data if the...
RemoveClusterAndReassignVariantsWithEstepRemove a (or more) cluster and reassign its data if the...
RemoveClusterAndReassignVariantsWithEstep_svRemove a (or more) cluster and reassign its data if the...
RunCcubePipelineRun Ccube analysis
RunPostAssignPipelineA pipeline to post assign events.
vbgmmVariational Bayesian Gaussian mixture model (VB-SMM)
vbsmmVariational Bayesian Student-t mixture model (VB-SMM)
WritePcawgFormatsWrite files in PCAWG-11 formats, works for both CcubeCore and...
WritePcawgFormats_svWrite files in PCAWG-11 formats, works for both CcubeCore and...
keyuan/ccube documentation built on May 20, 2019, 9:20 a.m.