Fig. 3. AUC boxplots for LDpred in simulation experiments with correlated SNPs.

Each box represents 50 replications and is presented as median values and the first and third quartiles. The upper/lower whisker extends from the hinge to the largest/smallest value at most 1.5 IQR from the hinge. We changed the proportion of risk SNPs from {1, 3e − 1, 1e − 1, 3e − 2, 1e − 2, 3e − 3, 1e − 3, 3e − 4, 1e − 4, 3e − 5, 1e − 5} and the sample sizes of training data from 4000 to 10,000. The grey, yellow, and red panels represent AUC predicted from PRStuning, AUC calculated from testing data, and the unadjusted AUC, respectively. Source data are provided as a Source Data file.