runGetDirichletProcessInfo: Create the DPClust input file

In shaghayeghsoudi/DPclust3p_Customised: Dirichlet Process Clustering Pre-Processing Package

Create the DPClust input file

Description

Function that takes allele counts and a copy number profile to estimate mutation copy number, cancer cell fraction and multiplicity for each point mutation.

Usage

runGetDirichletProcessInfo(
  loci_file,
  allele_frequencies_file,
  cellularity_file,
  subclone_file,
  gender,
  SNP.phase.file,
  mut.phase.file,
  output_file
)

Arguments

loci_file	Simple four column file with chromosome, position, reference allele and alternative allele
allele_frequencies_file	Output file from alleleCounter on the specified loci
cellularity_file	Full path to a Battenberg rho_and_psi output file
subclone_file	Full path to a Battenberg subclones.txt output file
gender	Specify male or female
SNP.phase.file	Output file from mut_mut_phasing, supply NA (as char) when not available
mut.phase.file	Output file from mut_cn_phasing, supply NA (as char) when not available
output_file	Name of the output file

Author(s)

sd11

shaghayeghsoudi/DPclust3p_Customised documentation built on March 18, 2022, 5:28 a.m.