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Pseudo-R²

Definition
AI-generated

Pseudo-R² is a class of goodness-of-fit measures for models with non-Gaussian outcomes (e.g. logistic regression) that mimic the interpretability of R² by scaling log-likelihood improvement relative to a null model; common variants include McFadden’s and Nagelkerke’s definitions.

Topics
Epidemiology
Synonyms
Pseudo R²
Related
Case-Control Study Liability Scale Net Reclassification Improvement (NRI)

Why it matters in GWAS

Binary-trait association and PRS prediction papers sometimes report pseudo-R² to quantify variance explained on the observed scale, alongside liability-scale R² for disease traits.

Example usage

"The full logistic model including PRS achieved Nagelkerke pseudo-R² = 0.12 for case-control status."

Case-Control Study Liability Scale Net Reclassification Improvement (NRI) Observed Scale Polygenic Risk Score (PRS) SNP Heritability
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References

  • Choi SW, Mak TSH, O'Reilly PF. (2020). Tutorial: a guide to performing polygenic risk score analyses. Nat Protoc. https://doi.org/10.1038/s41596-020-0353-1

  • Uffelmann E, et al. (2021). Genome-wide association studies. Nat Rev Methods Primers. https://doi.org/10.1038/s43586-021-00056-9

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