CNA_processing.R: fold change bug for clinical samples

[shguturu]

CNA script fails for subset of patients where fold change is not available from the data file. CNA_final_call_set folder and {sample_id}_cna_final_call_set.txt files are not produced

Error in `filter()`:
ℹ In argument: `fc != 0`.
Caused by error:
! object 'fc' not found
Backtrace:
     ▆
  1. ├─global CNA_processing(fread(master.ref), results.dir, dmp.dir, gene_set)
  2. │ └─... %>% data.table()
  3. ├─data.table::data.table(.)
  4. ├─base::unique(.)
  5. ├─dplyr::transmute(., Hugo_Symbol, CNA_tumor, cmo_patient_id, dmp_patient_id)
  6. ├─base::merge(...)
  7. ├─dplyr::mutate(...)
  8. ├─dplyr::filter(., fc != 0)
  9. ├─dplyr:::filter.data.frame(., fc != 0)
 10. │ └─dplyr:::filter_rows(.data, dots, by)
 11. │   └─dplyr:::filter_eval(...)
 12. │     ├─base::withCallingHandlers(...)
 13. │     └─mask$eval_all_filter(dots, env_filter)
 14. │       └─dplyr (local) eval()
 15. └─base::.handleSimpleError(`<fn>`, "object 'fc' not found", base::quote(NULL))
 16.   └─dplyr (local) h(simpleError(msg, call))
 17.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted