LogR_correction

Correct logR for msp1 fragment size bias and GC content

LogR_correction(
  dt_sample,
  dt_SNPs,
  build,
  chr_names,
  min_normal,
  fragments_file,
  replic_timing_file_prefix,
  n_cores
)

Arguments

dt_sample

Allelecounts output as a data.table

dt_SNPs

Allelecounts output subset to QC'ed SNP positions

build

Character variable corresponding to the reference genome version used for alignment

chr_names

Character variable with the seqlevels.

min_normal

Numerical with the minimum normal coverage threshold

fragments_file

CAMDAC reference MspI fragments file

replic_timing_file_prefix

CAMDAC reference replication timing files path and file name prefix

n_cores

Numerical value correspdonding to the number of cores for parallel processing

Author

Elizabeth Larose Cadieux