gc.correct: Correct the LogR estimates for GC content
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

gc.correct

R Documentation

Correct the LogR estimates for GC content

Description

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.

Usage

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"
)

Arguments

`samplename`	Name of the sample to be used to name columns
`infile.logr.baf`	String that points to the raw combined BAF and LogR file that is the result of `cel2baf.logr`
`outfile.tumor.LogR`	The filename of the file where the tumour LogR will be written
`outfile.tumor.BAF`	The filename of the file where the tumour BAF will be written
`outfile.normal.LogR`	The filename of the file where the normal LogR will be written
`outfile.normal.BAF`	The filename of the file where the normal BAF will be written
`outfile.probeBAF`	The filename of the file where the probe ids and their BAF will be saved
`snp6_reference_info_file`	String to the SNP6 reference info file that comes with Battenberg SNP6
`chr_names`	A vector of chromosome names that are to be used
`birdseed_report_file`	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)