cnfit_to_refit_suggestions: Create refit suggestions for a fit copy number profile
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

cnfit_to_refit_suggestions

R Documentation

Create refit suggestions for a fit copy number profile

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)