Table 6 Accuracy and execution time (in seconds) of Toxo and PyToxo for threshold, additive and multiplicative models with orders between 2 and 8 and different values of MAFs and heritability (\(h^2\))
From: PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models
Model | Order | MAF | h2 | PyToxo error | Toxo error | Best | PyToxo Time | Toxo Time | Speedup |
|---|---|---|---|---|---|---|---|---|---|
Threshold | 2 | 0.1 | 0.1 | 2.78\(\times 10^{-17}\) | 2.45\(\times 10^{-8}\) | PyToxo | 0.20 | 0.55 | 2.70 |
Threshold | 2 | 0.1 | 0.8 | 0 | 0 | Same | 0.18 | 0.23 | 1.22 |
Threshold | 2 | 0.4 | 0.1 | 1.11\(\times 10^{-16}\) | 0 | Toxo | 0.14 | 0.24 | 1.70 |
Threshold | 2 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 0 | Toxo | 0.14 | 0.22 | 1.57 |
Threshold | 3 | 0.1 | 0.1 | 1.39\(\times 10^{-17}\) | 1.70\(\times 10^{-7}\) | PyToxo | 0.39 | 0.31 | 0.79 |
Threshold | 3 | 0.1 | 0.8 | 0 | 3.44\(\times 10^{-9}\) | PyToxo | 0.37 | 0.71 | 1.91 |
Threshold | 3 | 0.4 | 0.1 | 0 | 0 | Same | 0.31 | 0.30 | 0.98 |
Threshold | 3 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 0 | Toxo | 0.32 | 0.29 | 0.92 |
Threshold | 4 | 0.1 | 0.1 | 0 | 7.41\(\times 10^{-7}\) | PyToxo | 0.81 | 0.52 | 0.65 |
Threshold | 4 | 0.1 | 0.8 | 0 | 1.60\(\times 10^{-8}\) | PyToxo | 0.80 | 0.92 | 1.15 |
Threshold | 4 | 0.4 | 0.1 | 2.78\(\times 10^{-17}\) | 0 | Toxo | 0.67 | 0.52 | 0.77 |
Threshold | 4 | 0.4 | 0.8 | 0 | 0 | Same | 0.67 | 0.53 | 0.77 |
Threshold | 5 | 0.1 | 0.1 | 0 | 1.41\(\times 10^{-6}\) | PyToxo | 1.95 | 1.99 | 1.02 |
Threshold | 5 | 0.1 | 0.8 | 1.11\(\times 10^{-16}\) | 5.71\(\times 10^{-8}\) | PyToxo | 2.04 | 2.34 | 1.15 |
Threshold | 5 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 0 | Toxo | 2.39 | 1.98 | 0.83 |
Threshold | 5 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 4.17\(\times 10^{-9}\) | PyToxo | 2.43 | 1.94 | 0.80 |
Threshold | 6 | 0.1 | 0.1 | 1.39\(\times 10^{-17}\) | 1.95\(\times 10^{-5}\) | PyToxo | 4.70 | 4.31 | 0.92 |
Threshold | 6 | 0.1 | 0.8 | 2.22\(\times 10^{-16}\) | 5.43\(\times 10^{-8}\) | PyToxo | 4.68 | 4.26 | 0.91 |
Threshold | 6 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 0 | Toxo | 6.64 | 4.29 | 0.65 |
Threshold | 6 | 0.4 | 0.8 | 0 | 5.05\(\times 10^{-9}\) | PyToxo | 6.59 | 4.70 | 0.71 |
Threshold | 7 | 0.1 | 0.1 | 1.39\(\times 10^{-17}\) | 3.81\(\times 10^{-5}\) | PyToxo | 11.69 | 18.27 | 1.56 |
Threshold | 7 | 0.1 | 0.8 | 1.11\(\times 10^{-16}\) | 1.58\(\times 10^{-8}\) | PyToxo | 11.62 | 18.68 | 1.61 |
Threshold | 7 | 0.4 | 0.1 | 4.16\(\times 10^{-17}\) | 0 | Toxo | 18.50 | 18.33 | 0.99 |
Threshold | 7 | 0.4 | 0.8 | 2.22\(\times 10^{-16}\) | 0 | Toxo | 18.49 | 18.70 | 1.01 |
Threshold | 8 | 0.1 | 0.1 | 2.78\(\times 10^{-17}\) | \(2.42\times 10^{-4}\) | PyToxo | 28.72 | 39.03 | 1.35 |
Threshold | 8 | 0.1 | 0.8 | 1.11\(\times 10^{-16}\) | 1.29\(\times 10^{-6}\) | PyToxo | 28.70 | 39.23 | 1.37 |
Threshold | 8 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 3.51\(\times 10^{-8}\) | PyToxo | 52.58 | 38.91 | 0.74 |
Threshold | 8 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 0 | Toxo | 52.69 | 38.88 | 0.74 |
Additive | 3 | 0.1 | 0.1 | 1.39\(\times 10^{-17}\) | 1.05\(\times 10^{-6}\) | PyToxo | 2.13 | 3.04 | 1.43 |
Additive | 3 | 0.1 | 0.8 | 2.22\(\times 10^{-16}\) | 3.26\(\times 10^{-5}\) | PyToxo | 1.90 | 1.67 | 0.88 |
Additive | 3 | 0.4 | 0.1 | 9.71\(\times 10^{-17}\) | 0 | Toxo | 1.81 | 1.53 | 0.85 |
Additive | 3 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 1.62\(\times 10^{-7}\) | PyToxo | 1.76 | 1.62 | 0.92 |
Additive | 4 | 0.1 | 0.1 | 2.78\(\times 10^{-17}\) | 5.54\(\times 10^{-4}\) | PyToxo | 3.04 | 8.72 | 2.87 |
Additive | 4 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 0 | Toxo | 3.16 | 4.94 | 1.56 |
Additive | 4 | 0.4 | 0.8 | 0 | 0 | PyToxo | 3.20 | 4.72 | 1.47 |
Additive | 5 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 2.66\(\times 10^{-8}\) | PyToxo | 6.14 | 8.80 | 1.43 |
Additive | 6 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 6.37\(\times 10^{-7}\) | PyToxo | 13.19 | 22.60 | 1.71 |
Additive | 7 | 0.4 | 0.1 | 0 | 4.69\(\times 10^{-7}\) | PyToxo | 25.86 | 51.82 | 2.00 |
Multiplicative | 2 | 0.1 | 0.1 | 0 | 4.16\(\times 10^{-6}\) | PyToxo | 0.67 | 2.84 | 4.25 |
Multiplicative | 2 | 0.1 | 0.8 | 0 | 1.20\(\times 10^{-7}\) | PyToxo | 0.69 | 1.01 | 1.47 |
Multiplicative | 2 | 0.4 | 0.1 | 0 | 0 | Same | 0.71 | 1.01 | 1.43 |
Multiplicative | 2 | 0.4 | 0.8 | 0 | 4.88\(\times 10^{-9}\) | PyToxo | 0.64 | 1.00 | 1.56 |
Multiplicative | 3 | 0.1 | 0.1 | 1.25\(\times 10^{-16}\) | 7.51\(\times 10^{-4}\) | PyToxo | 1.62 | 5.88 | 3.62 |
Multiplicative | 3 | 0.1 | 0.8 | 0 | 3.59\(\times 10^{-6}\) | PyToxo | 1.62 | 3.95 | 2.44 |
Multiplicative | 3 | 0.4 | 0.1 | 4.16\(\times 10^{-17}\) | 1.63\(\times 10^{-7}\) | PyToxo | 1.66 | 2.96 | 1.78 |
Multiplicative | 3 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 1.39\(\times 10^{-8}\) | PyToxo | 1.59 | 3.48 | 2.18 |
Multiplicative | 4 | 0.1 | 0.1 | 8.33\(\times 10^{-17}\) | 3.29\(\times 10^{-17}\) | PyToxo | 4.69 | 83.18 | 17.75 |
Multiplicative | 4 | 0.1 | 0.8 | 3.33\(\times 10^{-16}\) | 3.57\(\times 10^{-5}\) | PyToxo | 4.34 | 81.94 | 18.88 |
Multiplicative | 4 | 0.4 | 0.1 | 1.39\(\times 10^{-17}\) | 1.08\(\times 10^{-6}\) | PyToxo | 4.55 | 54.42 | 11.94 |
Multiplicative | 4 | 0.4 | 0.8 | 1.11\(\times 10^{-16}\) | 3.60\(\times 10^{-8}\) | PyToxo | 4.77 | 51.33 | 10.75 |