gc.correct.wgs: Function to correct LogR for waivyness that correlates with...

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

Function to correct LogR for waivyness that correlates with GC content

Description

Function to correct LogR for waivyness that correlates with GC content

Usage

gc.correct.wgs(
  Tumour_LogR_file,
  outfile,
  correlations_outfile,
  gc_content_file_prefix,
  replic_timing_file_prefix,
  chrom_names,
  recalc_corr_afterwards = F
)

Arguments

Tumour_LogR_file	String pointing to the tumour LogR output
outfile	String pointing to where the GC corrected LogR should be written
correlations_outfile	File where correlations are to be saved
gc_content_file_prefix	String pointing to where GC windows for this reference genome can be found. These files should be split per chromosome and this prefix must contain the full path until chr in its name. The .txt extension is automatically added.
replic_timing_file_prefix	Like the gc_content_file_prefix, containing replication timing info (supply NULL if no replication timing correction is to be applied)
chrom_names	A vector containing chromosome names to be considered
recalc_corr_afterwards	Set to TRUE to recalculate correlations after correction

Author(s)

jdemeul, sd11

Wedge-lab/battenberg documentation built on July 31, 2023, 1:32 p.m.