cel2baf.logr: Transform cel files into BAF and LogR

In Wedge-lab/battenberg: Battenberg subclonal copy number caller

Transform cel files into BAF and LogR

Description

This function takes a cel file from a tumour and a matched normal and extracts the BAF and LogR, which is saved into a single file. The gc.correct function can read that file and transforms it into separate BAF and LogR files that both Battenberg and ASCAT can use.

Usage

cel2baf.logr(
  normal_cel_file,
  tumour_cel_file,
  output_file,
  snp6_reference_info_file,
  apt.probeset.genotype.exe = "apt-probeset-genotype",
  apt.probeset.summarize.exe = "apt-probeset-summarize",
  norm.geno.clust.exe = "normalize_affy_geno_cluster.pl"
)

Arguments

normal_cel_file	String that points to the cel file containing the matched normal data
tumour_cel_file	String that points to the cel file containing the tumour data
output_file	String where the BAF and LogR should be written
snp6_reference_info_file	String to the SNP6 reference info file that comes with Battenberg SNP6
apt.probeset.genotype.exe	Path to the apt.probeset.genotype executable (Default $PATH)
apt.probeset.summarize.exe	Path to the apt.probeset.summarize executable (Default $PATH)
norm.geno.clust.exe	Path to the normalize_affy_geno_cluster.pl script (Default $PATH)

Author(s)

sd11

Wedge-lab/battenberg documentation built on April 5, 2025, 9:15 a.m.