aoutools: Tools for All of Us Researcher Workbench

aoutools is a Python library designed to simplify common analysis tasks on the All of Us Researcher Workbench.

Note

Disclaimer: This project is not affiliated with, endorsed by, or sponsored by the All of Us Research Program. The software is provided as is, without warranty. It is in an early stage of development, and its functions, APIs, and signatures may change periodically.

Overview

aoutools aims to provide a suite of high-level functions designed to make All of Us data analyses more accessible. The initial release focuses on the aoutools.prs submodule for calculating Polygenic Risk Scores (PRS).

Getting Started

• Installation
  • From PyPI
  • From GitHub
  • Troubleshooting
• How-To Guides
  • How-To: Calculate a Polygenic Risk Score (PRS)
  • How-To: Use the calculate_pgs Workflow
  • How-To: Using the download_pgs Function

Understanding

• How PRS Scoring Works
  • The basic idea
  • How the data is stored
  • Trap 1: The effect allele can be either the reference or the alternate
  • Trap 2: When the effect allele is the reference, most people are invisible
  • Trap 3: Sites with more than one alternate allele
  • Trap 4: An unknown genotype is not a reference match
  • Trap 5: The same variant can be written more than one way
  • A gallery of variant shapes
  • A note on the weights themselves
  • Running efficiently on a very large dataset
  • What aoutools does not do
  • In short

Reference

• API Reference
  • aoutools.prs
  • aoutools (workbench)