ABC: A Better Coefficient of Determination for Genetic Profile Analysis

Input

Prevalence of disease in the population
The proportion of cases in the case-control sample from which R2N was estimated
Nagelkerke's R2N value obtained from a logistic regression in a case-control sample

Result

$$h^2_{l}$$, proportion of variance in liability explained by the predictor:

Via equation 15 of Lee et al. (see citation) convert Nagelkerke's R2 to an R2 in liability at the population level.

Citation

Lee SH, Goddard ME, Wray NR, Visscher PM. (2012) A better coefficient of determination for genetic profile analysis. Genet Epidemiol. 2012 Apr