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Todo:

  • Change all files to load in the data in data/cohort_clin_data
  • Create a makefile to automate the running of this code.
  • Switch brca_regimens.rmd and process_drug_data.R away from using data lists, and use the individual datasets instead.
  • It's not a rare event at all (>50 cases) for participants to have a report date which is after their death or loss to followup. Why is this? Does this indeed challenge our assumptions?
  • Update all reports to read in the distinctly filtered survival datasets.

Curiousities:

  • Are GENIE-MSK-P-0017706-T02-IM6 and GENIE-MSK-P-0017706-T01-IM6 totally identical?