Create refit suggestions for a fit copy number profile — cnfit_to_refit

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.

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

sd11