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 ( 2).

Winham et al.

Winham et al. BMC Bioinformatics 2012 13:164   doi:10.1186/1471-2105-13-164

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