ccube

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Documentation for package ‘ccube’ version 1.0

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AnnotateCcubeResults Annotate mydata with Ccube results
AnnotateCcubeResults_sv Annotate mydata with CcubeSV results
Assign Assign data to centers
AssignWithCcube Computing responsibilities (assignment probabilities) with modified Ccube VBEM-step
AssignWithCcube_sv Computing responsibilities (assignment probabilities) with modified Ccube_sv VBEM-step
bsxfun.se bsxfun pracma with single expansion (real Matlab style)
CcubeCore Run Ccube Core function
CcubeSVCore Run Ccube Core function for SV
ccube_m6 Run Ccube with model 6: Normal-Binomial. TODO: to be removed in the final release
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 underflow
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 cluster is nonempty
RemoveClusterAndReassignVariantsWithEMsteps Remove a (or more) cluster and reassign its data if the cluster is nonempty
RemoveClusterAndReassignVariantsWithEMsteps_sv Remove a (or more) cluster and reassign its data if the cluster is nonempty
RemoveClusterAndReassignVariantsWithEstep Remove a (or more) cluster and reassign its data if the cluster is nonempty
RemoveClusterAndReassignVariantsWithEstep_sv Remove a (or more) cluster and reassign its data if the cluster is nonempty
RemoveClusterAndReassignVariants_sv Remove a (or more) cluster and reassign its data if the cluster is nonempty
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 ccube_m6 output
WritePcawgFormats_sv Write files in PCAWG-11 formats, works for both CcubeCore and ccube_m6 output