Figure 5.

Inferred predictive performance $r^2$ in the UK Biobank

This compares the $r^2$ inferred from the Gibbs sampler of LDpred2-auto (material and methods) versus the ones obtained in the test set, for all 248 phenotypes defined from the UKBB. These are stratified by the SNP heritability estimated from LDpred2-auto. Green dashed lines represent the 1:1 line. The 95% CI for the LDpred2-auto estimate is obtained from the 2.5% and 97.5% quantiles of all the $r^2$ estimates from the iterations (after burn-in) of the chains kept. The 95% CI for $r^2$ in the test set is obtained from bootstrap. Colors represent the number of chains kept (out of 50). “F_height” and “M_height” use females and males only, respectively (in both GWAS and test sets).