Welcome to pyPheWAS’s documentation!

The pyPhewas module is used to execute a variety of different analyses on large sets of patient phenotype data.

Features

• Data cleaning and preparation
• Run logarithmic regressions on patient data
• Plot results

Latest Release: pyPheWAS 3.0.0

This release includes:

• Support for both ICD 9 and ICD 10
• All 3 regression types (binary, count, & duration) optimized for big data
• pyPhewasPipeline: a streamlined combination of pyPhewasLookup, pyPhewasModel, and pyPhewasPlot
• Compatibility with Python 3
• Age matching now saves the explicit mapping between controls/cases in addition to the resulting group file
• Operation of the ICD censoring function matches the description in the documentation
• Minor bug fixes

Support

• Issue Tracker: github.com/MASILab/pyPheWAS/issues
• Source Code: github.com/MASILab/pyPheWAS

If you are having issues, please let us know! Email me at:

cailey.i.kerley@vanderbilt.edu

License

This project is licensed under the MIT license.

Contents

• Tutorial
  • Basics
  • Research Tools
  • Data Preparation
• Source Documentation
  • pyPheWAS – Root package
  • pyPheWAS.pyPhewasv2 – pyPhewas functions file
  • pyPheWAS.pyPhewasCore – pyPhewas Research Tools file

Indices and tables

• Index
• Search Page
• Module Index