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Generating a Phenotype Codelist

Overview

This page provides an example R script that can be adapted to generate a phenotype codelist for this repository. This codelist-generating R script template is for CPRD Gold and Aurum. The script is intended as a starting point for contributors and should not be used to generate codelists without careful review and adaptation.

💡 Tip: Search 🔴 in the script to jump directly to sections that need changing for your phenotype.

Download the Template

Download the R script here:

What This Script Is For

This R script helps contributors:

  • Identify relevant clinical codes for a phenotype
  • Document inclusion and exclusion logic
  • Generate a structured codelist for review
  • Adapt the workflow for a new phenotype

How to Use It

  1. Download the template R script and open it in R or RStudio.
  2. Set up and load the required data (see Inputs below).
  3. Replace the example phenotype content with your own phenotype definition.
  4. Update the inclusion and exclusion logic as needed.
  5. Search for new relevant medical codes and compare with multiple reference lists.
  6. Create and update the codelists, then review the output carefully.
  7. Save the resulting codelist and associated metadata.
  8. Upload your codelist and supporting files to your repository.

What You Should Customise

Before using the script, review and adapt:

  • The phenotype name
  • The code search terms
  • The inclusion criteria
  • The exclusion criteria
  • Any reviewer notes
  • Metadata describing dataset, coding system, and intended use

Inputs

# File Description
1 CPRDAurumMedical.txt CPRD Aurum medical dictionary
2 CPRDGoldMedical.txt CPRD Gold medical dictionary
3 Aurum_Depression_codelist_20250725.txt Depression codelist from GitHub
4 Gold_Depression_codelist_20250725.txt Depression codelist from GitHub
5 hdrukcodelist.csv Depression phenotype from HDRUK library
6 qof.xlsm Quality and Outcomes Framework clusters list

Outputs

Intermediate Outputs (for clinical review)

File Description
aurum_depression_codelist_15042026_tobereviewed.csv Aurum codelist to be clinically reviewed
gold_depression_codelist_15042026_tobereviewed.csv Gold codelist to be clinically reviewed

Final Outputs

File Description
aurum_depression_codelist_15042026.txt Final depression codelist from Aurum
gold_depression_codelist_15042026.txt Final depression codelist from Gold
Depression_metadata_15042026.txt Metadata text file

When contributing a codelist, include:

  • The generated codelist file
  • A metadata file describing the phenotype
  • The codelist-generating script
  • A citation file (CITATION.cff) where possible

Notes for Contributors

Please treat this script as a template rather than a final validated definition. All generated codelists should be checked for:

  • Correctness
  • Completeness
  • Reproducibility
  • Clinical and research appropriateness where relevant