Table 2. Running times for eight pathway analysis programs for GWAS summary data.
Method | Time | Permutation |
---|---|---|
GSA-SNP2 | 1.53 min | |
GSA-SNP1 | 1.49 min | |
MAGMA-mean | 3.03 min | |
MAGMA-top1 | 34.85 min | |
MAGMA-multi | 41.85 min | |
iGSEA4GWAS | 30 min | |
MAGENTA | 114.18 min | 10 000 |
Gowinda (P = 0.001) | 0.62 min | 10 000 |
Gowinda (P = 0.01) | 0.80 min | 10 000 |
Gowinda (P = 0.05) | 2.01 min | 10 000 |
INRICH (P1 = 1E-6) | 0.85 min | 10 000 |
INRICH (P1 = 1E-4) | 2.41 min | 10 000 |
sARTP | 10.41 days | 100 000 |