dumpCounts.maf: Run alleleCount Dump allele counts from maf file

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

Run alleleCount Dump allele counts from maf file

Description

Dump allele counts stored in the sample columns of the maf file. Output will go into a file supplied as tumour_outfile and optionally normal_outfile. It will be a fully formatted allele counts file as returned by alleleCounter.

Usage

dumpCounts.maf(
  maf_file,
  tumour_outfile,
  normal_outfile = NA,
  samplename = NA,
  dummy_alt_allele = NA,
  dummy_ref_allele = NA
)

Arguments

maf_file	The maf file to read in
tumour_outfile	File to save the tumour counts to
normal_outfile	Optional parameter specifying where the normal output should go
samplename	Optional parameter specifying the samplename to be used for matching the right column in the maf
dummy_alt_allele
dummy_ref_allele

Author(s)

sd11

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