This function performs part of the Battenberg SNP6 pipeline: Extract BAF and logR from the CEL files and performing GC content correction.
prepare_snp6(
tumour_cel_file,
normal_cel_file,
tumourname,
chrom_names,
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",
birdseed_report_file = "birdseed.report.txt",
genomebuild = "hg19"
)Full path to a CEL file containing the tumour raw data
Full path to a CEL file containing the normal raw data
Identifier to be used for tumour output files
A vector containing the names of chromosomes to be included
Full path to the SNP6 reference info file
Full path to the apt.probeset.genotype executable (Default: expected in $PATH)
Full path to the apt.probeset.summarize executable (Default: expected in $PATH)
Full path to the norm.geno.clust.exe executable (Default: expected in $PATH)
Name of the birdseed output file. This is a temp output file of one of the internally called functions of which the name cannot be defined. Don't change this parameter. (Default: birdseed.report.txt)