This function performs GC correction of the LogR data. Sometimes a wave pattern is observed there that correlates with GC content. Internally it uses the ASCAT gc correction function.
gc.correct(
samplename,
infile.logr.baf,
outfile.tumor.LogR,
outfile.tumor.BAF,
outfile.normal.LogR,
outfile.normal.BAF,
outfile.probeBAF,
snp6_reference_info_file,
chr_names,
birdseed_report_file = "birdseed.report.txt",
genomebuild = "hg19"
)Name of the sample to be used to name columns
String that points to the raw combined BAF and LogR file that is the result of cel2baf.logr
The filename of the file where the tumour LogR will be written
The filename of the file where the tumour BAF will be written
The filename of the file where the normal LogR will be written
The filename of the file where the normal BAF will be written
The filename of the file where the probe ids and their BAF will be saved
String to the SNP6 reference info file that comes with Battenberg SNP6
A vector of chromosome names that are to be used
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)