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Welcome to the PIGEON wiki!

Overview of PIGEON

PIGEON (PolygenIc Gene-Environment interactiON) is a Python3-based command line tool for estimating polygenic gene-environment (GxE) interactions using GWIS (and GWAS) summary statistics.

The PIGEON software can be used to

• estimate the proportion of phenotypic variance explained by genome-wide GxE interactions.
• perform hypothesis-free scans for PGSxE across many PGS (without the need to calculate PGS).

In this wiki, we provided short tutorials describing the two basic functions (estimating GxE variance components and hypothesis-free scans for PGSxE) in PIGEON.

Contents of the wiki

• Install PIGEON and prepare the data required.
• Estimate GxE variance component
• Perform scans for PGSxE and covariant GxE
• Inference for polygenic GxE in the presence of G‐E correlations (rGE).