cnfit_to_refit_suggestions: Create refit suggestions for a fit copy number profile

In shaghayeghsoudi/Battenberg_customized: Battenberg subclonal copy number caller

Description

This function takes a fit copy number profile and generates refit suggestions for a future rerun. If there are clonal alterations above a specified size, then those written out as supplied as suggestions, otherwise a refit suggestion of an external purity value will be saved.

Usage

cnfit_to_refit_suggestions(
  samplename,
  subclones_file,
  rho_psi_file,
  gamma_param,
  min_segment_size_mb = 2
)

Arguments

samplename	Samplename for the output file
subclones_file	File containing a fit copy number profile
rho_psi_file	File with rho and psi values
gamma_param	Platform gamma parameter
min_segment_size_mb	Minimum size of a segment in Mb to be considered for a refit suggestion (Default: 2)

Author(s)

sd11

shaghayeghsoudi/Battenberg_customized documentation built on Feb. 13, 2022, 4:10 a.m.