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Generating Phenotypes in the RAP

This directory contains iPython notebooks to reproduce some phenotypes used to train and evaluate the PRS release models used to generate the PRS in the UK Biobank PRS Release.*

Details on these phenotypes can be found in the Thompson et al publication https://www.medrxiv.org/content/10.1101/2022.06.16.22276246v1.

These notebooks can be run from within a DNANexus project to generate phenotypes that are resolved to your unique participant identifiers.

*Please note that these notebooks many not recapitulate the exact phenotypes used in the UKB PRS Release if the backing data changes (for example if UKB update data in a new release, or if samples are withdrawn)

Constructing your phenotype

Before attempting to run a pheconstructor file, please ensure that you have a DNANexus project prepared with the UKB data dispensed to a spark dataset.

  1. Select the file corresponding to either a disease phenotype (disease_pheconstructor.py) or a quantitative trait phenotype (qt_pheconstructor.py)and convert this file to a Jupyter notebook using jupytext. This can be done via the command line with the command jupytext --to ipynb [disease|qt]_pheconstructor.py
  2. Upload the notebook to your DNANexus project with dx upload [disease|qt]_pheconstructor.ipynb
  3. Upload the YAML of valid traits to your DNANexus project with dx upload [diseases|qt].yaml
  4. Start a JupyterLab instance from the DNANexus web interface, ensuring that it is running on a Spark cluster
  5. Open the pheconstructor notebook and replace the TRAIT_CODE variable in the first Python cell of this notebook with the trait of interest
  6. Replace the '<dataset_id>.dataset' string in the first Python cell with the ID of your UKB dataset
  7. Run the notebook - this should output the phenotype data to a CSV file named <TRAIT_CODE>_phenotype.csv, which is compatible with the UKB-PRET tool. If the Spark queries in the notebook fail, try increasing the number of cores and/or processing power of your instance

*For instruction on running your phenotype with ukb-pret in the DNANexus Research Analysis Platform, please refer to project README