Table 1.
FastQTL and Matrix eQTL running times
| Number of permutations | Matrix eQTL |
FastQTL |
||
|---|---|---|---|---|
| 1000 | 1000 | 500 | 100 | |
| GTEx_AS | 337.4 | 19 | 10.8 | 3.5 |
| GTEx_AT | 330.3 | 21 | 10.8 | 3.6 |
| GTEx_HLV | 312.4 | 15 | 8 | 3 |
| GTEx_L | 364.9 | 25.6 | 13.1 | 4 |
| GTEx_MS | 335.9 | 23.6 | 12.6 | 3.9 |
| GTEx_NT | 343.8 | 18.4 | 9.5 | 3.4 |
| GTEx_SSEL | 349.7 | 20.7 | 10.8 | 3.6 |
| GTEx_T | 358.1 | 22.3 | 11.8 | 3.9 |
| GTEx_WB | 340.5 | 25.5 | 13.7 | 4.1 |
| ALL | 3073 | 191.1 | 101.1 | 33 |
Table 1 shows the running times in CPU hours to produce the results shown in Figure 2e; nine GTEx datasets (column 1) processed with 1000 Matrix eQTL permutations (column 2) and FastQTL with 1000 (column 3), 500 (column 4) and 100 permutations (column 5). Total running times for all nine datasets together are shown in the last row.