Table 3 The predicted AUC values for C+T, LDpred, and LDpred2 with different parameters in the simulation experiment based on the UKBB data
From: Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data
C+T | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Threshold | 1 | 5e − 1 | 5e − 2 | 5e − 3 | 5e − 4 | 5e − 5 | 5e − 6 | 5e − 7 | 5e − 8 | ||
PRStuning | 0.789 | 0.790 | 0.816 | 0.830 | 0.834 | 0.835 | 0.835 | 0.835 | 0.835 | ||
Testing | 0.793 | 0.795 | 0.830 | 0.852 | 0.860 | 0.865 | 0.867 | 0.868 | 0.868 | ||
LDpred | |||||||||||
π | 1 | 3e − 1 | 1e − 1 | 3e − 2 | 1e − 2 | 3e − 3 | 1e − 3 | 3e − 4 | 1e − 4 | 3e − 5 | 1e − 5 |
PRStuning | 0.747 | 0.784 | 0.732 | 0.593 | 0.550 | 0.532 | 0.519 | 0.513 | 0.509 | 0.504 | 0.502 |
Testing | 0.790 | 0.813 | 0.749 | 0.588 | 0.548 | 0.527 | 0.518 | 0.509 | 0.506 | 0.500 | 0.506 |
LDpred2 | |||||||||||
π | 1 | 3e − 1 | 1e − 1 | 3e − 2 | 1e − 2 | 3e − 3 | 1e − 3 | 3e − 4 | 1e − 4 | 3e − 5 | 1e − 5 |
PRStuning | 0.768 | 0.777 | 0.767 | 0.781 | 0.767 | 0.837 | 0.890 | 0.919 | 0.875 | 0.915 | 0.926 |
Testing | 0.780 | 0.787 | 0.793 | 0.785 | 0.771 | 0.818 | 0.846 | 0.859 | 0.838 | 0.856 | 0.861 |
