Table 1 Contribution of HW disequilibrium to p value distribution, evaluated by regression analysis. Significant F tests (p < 0.05) demonstrating evidence of the contribution of HW disequilibrium to the p value distributions are shown in bold font
From: Assessing transmission ratio distortion in extended families: a comparison of analysis methods
Allb, c | Sequenceda, c | Nuclearb, c | |||||||
|---|---|---|---|---|---|---|---|---|---|
Method | TDT | PDT | FBAT | TDT | PDT | FBAT | TDT | PDT | FBAT |
Regression model of - log10 p values at all SNPs | |||||||||
R 2 full –R 2 reduced | 4.4 × \( {10}^{-4} \) | 3.6 × \( {10}^{-7} \) | 1.5 × \( {10}^{-6} \) | 0.0018 | 3.6 × \( {10}^{-8} \) | 2 × \( {10}^7 \) | 2.9 × \( {10}^{-6} \) | 8.26 × \( {10}^{-9} \) | 3.5 × \( {10}^{-7} \) |
# SNPse | 6.1 × \( {10}^6 \) | 5.6 × \( {10}^6 \) | 2.1 × \( {10}^6 \) | 3.2 × \( {10}^6 \) | 3 × \( {10}^6 \) | 8 × \( {10}^5 \) | 3.6 × \( {10}^6 \) | 2.1 × \( {10}^6 \) | 5 × \( {10}^5 \) |
Regression models of - log10 p values greater than 3 only | |||||||||
R 2 full –R 2 reduced | 0.002 | 8.4 × \( {10}^{-5} \) | 8.8 × \( {10}^{-4} \) | 0.0015 | \( {\mathrm{NA}}^f \) | 0.006 | 0.014 | 0.01 | 0.01 |
# SNPse | 8 × \( {10}^4 \) | 517 | 870 | 1777 | 11 | 19 | 3.3 × \( {10}^4 \) | 53 | 54 |
F-test p-valuesd | |||||||||
All SNPs | 0.00 | 0.16 | 0.07 | 0.00 | 0.74 | 0.69 | 0.00 | 0.89 | 0.68 |
P< \( {10}^{-3} \) | 0.00 | 0.84 | 0.38 | 0.10 | NAf | 0.82 | 0.00 | 0.49 | 0.50 |