RunDPClust_Beagle_nf: Runs DPClust using input provided in...

In afrangou/CleanCNA: Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.

Description

Clusters mutations by CCF using Dirichlet Process

Clusters mutations by CCF using Dirichlet Process

Usage

RunDPClust(
  sampledir,
  participantid,
  tumourplatekey,
  normalplatekey,
  dpinfofilepath,
  gender,
  vcffilepath,
  rhoandpsifilepath,
  subcloneshg38filepath,
  run
)

RunDPClust_Beagle_nf(
  tumourplatekey,
  normalplatekey,
  rhoandpsifilepath,
  dpinfofilepath,
  output_folder
)

Arguments

Tumour

platekey Germline platekey Filepath to purity and ploidy file from Battenberg Filepath to input file generated by GenerateDPinputt2BamAC_Beagle_nf Output directory

Value

Cluster assignment for all SNVs Plots showing the clusters OptimaInfo file summarising the clusters And the CCF and number of mutations assigned to each

Cluster assignment for all SNVs Plots showing the clusters OptimaInfo file summarising the clusters And the CCF and number of mutations assigned to each

afrangou/CleanCNA documentation built on Dec. 28, 2021, 8:21 p.m.