Fig. 1: AUC boxplots for P+T in the simulation experiments with independent SNPs.
From: Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data
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 p-value threshold from {1, 5e − 1, 5e − 2, 5e − 3, 5e − 4, 5e − 5, 5e − 6} and the sample sizes of training data from 4000 to 10,000. The grey, yellow, and red panels represent AUC predicted from PRStuning, AUC evaluated on testing data, and the unadjusted AUC directly estimated by plugging in the training summary statistics, respectively. The AUC evaluated on the testing data is the benchmark. PRStuning is able to yield AUC estimates comparable to the benchmark results. Source data are provided as a Source Data file.
