Table 3.
Simulation 3 results, Model 5
| Level of LD | MAF | Detection Definition | Raw MDA | Liaw MDA | SD MDA | Gini | LR P-value | |
|---|---|---|---|---|---|---|---|---|
| 1 |
Strong |
.294 |
Causal SNP |
0.05 |
0.09 |
0.05 |
0.02 |
0.09 |
| |
|
|
Causal Region |
0.2 |
0.19 |
0.21 |
0.1 |
0.3 |
| |
Strong |
.309 |
Causal SNP |
0.2 |
0.17 |
0.15 |
0.16 |
0.14 |
| |
|
|
Causal Region |
0.47 |
0.42 |
0.38 |
0.41 |
0.33 |
| 2 |
Weak |
.294 |
Causal SNP |
0.43 |
0.34 |
0.49 |
0.52 |
0.4 |
| |
Weak |
.281 |
Causal SNP |
0.35 |
0.25 |
0.35 |
0.42 |
0.29 |
| 3 |
Strong |
.294 |
Causal SNP |
0.06 |
0.09 |
0.04 |
0.04 |
0.12 |
| |
|
|
Causal Region |
0.32 |
0.27 |
0.27 |
0.14 |
0.41 |
| |
Weak |
.294 |
Causal SNP |
0.51 |
0.45 |
0.4 |
0.62 |
0.3 |
| 4 |
None |
.294 |
Causal SNP |
0.28 |
0.21 |
0.3 |
0.31 |
0.33 |
| None | .294 | Causal SNP | 0.29 | 0.27 | 0.3 | 0.31 | 0.29 |
Detection probability with and without LD for interaction effects only Model 5 for RF VIMs and logistic regression (LR). Total number of SNPs = 1,000, MAF ≈ 0.3. Average PE estimates range from 0.479 to 0.496 ( Additional file 2, Table B6).