Transform cel files into BAF and LogR

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.

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

sd11