Table 1.
Comparison of run-times (seconds and minutes) for SNPRelate, EIGENSTRAT and PLINK on a Linux system with two quad-core Intel processors (2.27 GHz) and 32 GB RAM
| Number of cores | Small seta |
Medium seta |
||||
|---|---|---|---|---|---|---|
| Method | 1 | 4 | 8 | 1 | 4 | 8 |
| PCA | ||||||
| SNPRelate | 11 s+ | 5 s+ | 3 s+ | 20 m+ | 8 m+ | 5 m+ |
| 1 sb | 1 sb | 1 sb | 12 mb | 12 mb | 12 mb | |
| EIGENSTRAT | 90 sc | — | — | 710 mc | — | — |
| MoM for IBD analysis | ||||||
| SNPRelate | 19 s | 6 s | 4 s | 30 m | 8 m | 5 m |
| PLINK | 980 s | — | — | 1630 m | — | — |
aSimulated 500 (small set) and 5000 (medium set) samples with 100 K SNPs.
bCalls the uniprocessor version of LAPACK in R to compute the eigenvalues and eigenvectors, taking 1 s and 12 m for the small and medium set, respectively.
cIncludes the computation time of calculating the eigenvalues and eigenvectors.