Table 2.
Simulation 3 results, Model 3
| Level of LD | MAF | Detection Definition | Raw MDA | Liaw MDA | SD MDA | Gini | LR P-value | |
|---|---|---|---|---|---|---|---|---|
| 1 |
Strong |
.294 |
Causal SNP |
0.13 |
0.12 |
0.14 |
0.08 |
0.21 |
| |
|
|
Causal Region |
0.38 |
0.3 |
0.4 |
0.29 |
0.49 |
| |
Strong |
.309 |
Causal SNP |
0.25 |
0.18 |
0.28 |
0.26 |
0.33 |
| |
|
|
Causal Region |
0.56 |
0.48 |
0.55 |
0.58 |
0.48 |
| 2 |
Weak |
.294 |
Causal SNP |
0.72 |
0.58 |
0.73 |
0.78 |
0.73 |
| |
Weak |
.281 |
Causal SNP |
0.66 |
0.56 |
0.71 |
0.79 |
0.76 |
| 3 |
Strong |
.294 |
Causal SNP |
0.15 |
0.13 |
0.11 |
0.08 |
0.21 |
| |
|
|
Causal Region |
0.5 |
0.46 |
0.52 |
0.39 |
0.71 |
| |
Weak |
.294 |
Causal SNP |
0.59 |
0.52 |
0.63 |
0.78 |
0.5 |
| 4 |
None |
.294 |
Causal SNP |
0.67 |
0.57 |
0.72 |
0.73 |
0.75 |
| None | .294 | Causal SNP | 0.68 | 0.6 | 0.67 | 0.7 | 0.76 |
Detection probability with and without LD for main effects only Model 3 for RF VIMs and logistic regression (LR). Total number of SNPs = 1,000, MAF ≈ 0.3. Average PE estimates range from 0.458 to 0.477 ( Additional file 2, Table B6).