Calculate refit values from a refit suggestion — suggest

Use this function to calculate the refit values from a refit suggestion.

suggest_refit(
  subclones_file,
  segment_chrom,
  segment_pos,
  new_nMaj,
  new_nMin,
  rho,
  gamma_param
)

Arguments

subclones_file: A Battenberg subclones.txt file
segment_chrom: Chromsome of the segment to use for refitting
segment_pos: Position within the start/end coordinates of the segment to use for refitting
new_nMaj: Major allele copy number
new_nMin: Minor allele copy number
rho: Sample rho parameter
gamma_param: Platform gamma parameter

A list with a field for rho and psi_t

sd11