Table 2.
The execution time (in s) of epistasis algorithms for 2000 samples and different numbers of SNVs.
| Order of epistasis | Algorithm | Number of SNVs | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 100 | 200 | 500 | 1000 | 2000 | 5000 | 10,000 | 20,000 | 50,000 | ||
| 2-SNV | BitEpi | 1 | 1 | 1 | 1 | 1 | 4 | 11 | 40 | 227 |
| BOOST | 1 | 1 | 1 | 1 | 1 | 1 | 4 | 15 | 56 | |
| MDR | 1 | 1 | 2 | 6 | 29 | 148 | 390 | 2619 | – | |
| 3-SNV | BitEpi | 1 | 1 | 4 | 28 | 221 | – | – | – | – |
| MPI3SNP | 1 | 1 | 6 | 47 | 375 | – | – | – | – | |
| MDR | 3 | 14 | 212 | 2121 | – | – | – | – | – | |
| 4-SNV | BitEpi | 1 | 15 | 460 | – | – | – | – | – | – |
| MDR | 51 | 834 | – | – | – | – | – | – | – | |
The process is killed if it takes more than an hour to complete and the execution time is not measured. If the execution time is less than a second it is reported as 1 in this table. All programs are executed with 16 parallel threads. Highlighted execution times are used to compute the average test time (see Fig. 3).