Table 6.
Association analysis max(T) permutation test times (sec)
| Other parameter(s) | Dataset | Machine | PLINK 1.07 | PERMORY 1.1 | PLINK 1.90 | Ratio |
|---|---|---|---|---|---|---|
| –trend (C/C) | synth1 | Mac-2 | ∼20 k | 18.7 | 1.1 k | |
| Mac-12 | ∼16 k | 2.8 | 5.7 k | |||
| Linux32-2 | ∼21 k | 65.0 | 320 | |||
| Linux64-512 | ∼17 k | 285.0 | 2.8 | |||
| Win32-2 | ∼35 k | 1444.2 | 61.5 | |||
| Win64-2 | ∼25 k | 889.7 | 14.4 | |||
| synth2 | Mac-2 | ∼170 k | 42.4 | 4.0 k | ||
| Mac-12 | ∼180 k | 6.4 | 28 k | |||
| Linux32-2 | ∼410 k | 391.0 | 1.0 k | |||
| Linux64-512 | ∼200 k | 580.9 | 13.7 | |||
| Win32-2 | ∼1100 k | 2362.5 | 198.0 | |||
| Win64-2 | ∼370 k | 1423.6 | 34.0 | |||
| –fisher (C/C) | synth1 | Mac-2 | ∼150 k | 21.9 | 6.9 k | |
| Mac-12 | ∼150 k | 3.7 | 41 k | |||
| Linux32-2 | ∼170 k | 57.8 | 2.9 k | |||
| Linux64-512 | ∼120 k | 3.4 | 35 k | |||
| Win32-2 | ∼440 k | 64.9 | 6.8 k | |||
| Win64-2 | ∼200 k | 22.0 | 9.1 k | |||
| synth2 | Mac-2 | ∼890 k | 49.8 | 18 k | ||
| Mac-12 | ∼690 k | 7.6 | 91 k | |||
| Linux32-2 | ∼1300 k | 393.7 | 3.3 k | |||
| Linux64-512 | ∼720 k | 13.0 | 55 k | |||
| Win32-2 | ∼3600 k | 208.3 | 17 k | |||
| Win64-2 | ∼1700 k | 35.6 | 48 k | |||
| –assoc (QT) | synth1 | Mac-2 | ∼30 k | 148.0 | 200 | |
| Mac-12 | ∼22 k | 22.6 | 970 | |||
| Linux32-2 | ∼68 k | 847.2 | 80 | |||
| Linux64-512 | ∼29 k | 29.2 | 990 | |||
| Win32-2 | ∼58 k | 896.1 | 65 | |||
| Win64-2 | ∼36 k | 264.2 | 140 | |||
| –assoc lin (QT) | synth1 | Mac-2 | 606.8 | |||
| Mac-12 | 34.7 | |||||
| Linux32-2 | 3212.6 | |||||
| Linux64-512 | 1259.8 | 46.4 | 27.2 | |||
| Win32-2 | 2115.7 | 3062.7 | 0.69 | |||
| Win64-2 | 972.6 | 336.6 | 2.89 |
All runs are with 10000 permutations and –seed 1. The PLINK 1.9 implementation extends Pahl et al.’s PERMORY algorithm [29] with multithreading (note the 12- and 512-core machine results) and additional low-level optimizations.