From: A comparison of genomic profiles of complex diseases under different models
Genotype-based, holdout approach | Haplotype-based, holdout approach | ||||||||
---|---|---|---|---|---|---|---|---|---|
p-value filtering | Top 100 SNPs | ||||||||
Disease | AUC | Learning | p-value | AUC | Learning | AUC | Learning | Haplotype | Threshold |
machine | threshold | machine | machine | length | p-value | ||||
BD | 0.6222 | LR wGRS | 15e-2 | 0.553 | RR | 0.6873 | AdaBoostM1-add. | 3 | 1e-4 |
CAD | 0.611 | 20RF | 1e-5 | 0.582 | sSVM | 0.5761 | 20RF-rec. | 3 | 1e-7 |
HT | 0.5776 | AdaBoostM1 | 15e-2 | 0.559 | lasso | 0.5573 | NBC-all | 5 | 1e-5 |
IBD | 0.6136 | AdaBoostM1 | 1e-5 | 0.587 | RR | 0.6213 | AdaBoostM1-rec. | 2 | 1e-5 |
RA | 0.8152 | AdaBoostM1 | 1e-5 | 0.736 | GLM AIC | 0.8024 | AdaBoostM1-add. | 2 | 1e-5 |
T1D | 0.8615 | AdaBoostM1 | 1e-5 | 0.793 | GLM AIC | 0.8682 | AdaBoostM1-add. | 3 | 1e-6 |
T2D | 0.6134 | AdaBoostM1 | 1e-3 | 0.576 | LR wGRS | 0.6372 | AdaBoostM1-add. | 2 | 1e-4 |