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Table 1 Median predicted mean square errors for calculated from the 100 randomly generated testing sets

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

  1. CV, common variant; RV, rare variant; SNP, single nucleotide polymorphism.