pyPheWAS Explorer Setup

Exactly like the PheWAS Tools, the Explorer requires a group file and a phenotype file, the formats of which may be found in the File Formats section. These files must be called group.csv and icds.csv, respectively, and be saved within the same directory on your filesystem.

Note

At this time, the Explorer can only parse numeric group variables. Categorical variables (e.g. sex, race) must be converted to numeric categories before launching pyPheWAS Explorer.

Launching the Explorer

The script pyPhewasExplorer is installed with the pyPheWAS package to launch the Explorer. This script accepts only two input arguments:

  • --indir: Path to input directory [default: current directory]
  • --response: Column name from group.csv to use as the dependent variable [default: target]

Example:

pyPhewasExplorer --indir /Users/me/Documents/EMRdata/ --response ADHD

To launch the Explorer, run the launch script as shown above and then open http://localhost:8000/ in a web browser (preferably Google Chrome).