From: Does the inclusion of rare variants improve risk prediction?
 | Top 10 SNPs | Top 100 SNPs | Top 1000 SNPs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Regression method | CV only | RV only | CV = 10; RV >0 | CV >0; RV = 10 | CV only | RV only | CV = 100; RV >0 | CV >0; RV = 100 | CV only | RV only | CV = 1000; RV >0 | CV >0; RV = 1000 |
OLS | 3.723 | 0.719 | 1.856 | 0.722 | 107.775 | 24 | 98.109 | 21.748 | 370644.875 | 311336.868 | 37064.875 | 63274.28 |
SCAD | 0.701 | 0.674 | 0.636 | 0.625 | 0.657 | 0.664 | 0.625 | 0.635 | 0.641 | 0.656 | 0.625 | 0.639 |
LASSO | 0.691 | 0.661 | 0.613 | 0.612 | 0.649 | 0.644 | 0.601 | 0.616 | 0.632 | 0.625 | 0.608 | 0.611 |
Elastic net (α= 0.5) | 0.689 | 0.661 | 0.610 | 0.610 | 0.646 | 0.643 | 0.601 | 0.613 | 0.630 | 0.619 | 0.608 | 0.610 |
Ridge | 0.681 | 0.658 | 0.644 | 0.640 | 0.664 | 0.680 | 0.641 | 0.672 | 0.778 | 0.780 | 0.742 | 0.741 |
TLP | 0.688 | 0.657 | 0.616 | 0.621 | 0.652 | 0.641 | 0.618 | 0.617 | 0.653 | 0.633 | 0.653 | 0.607 |