suggest_refit: Calculate refit values from a refit suggestion

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

Calculate refit values from a refit suggestion

Description

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

Usage

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

Value

A list with a field for rho and psi_t

Author(s)

sd11

Wedge-Oxford/battenberg documentation built on Aug. 4, 2023, 6:27 p.m.