Skip to main content

Table 4 Average time needed to exhaustively test one/all 1.25×10 11 pairs among 500,000 SNPs using a single-core CPU computer

From: Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis

Software Time for one/all SNPs (single core)
MB-MDR [16] 5×10-3 s/20 years [31]
PLINK Epistasis [7] 2×10-4 s/289 days [5]
PLINK FastEpistasis [8] 2×10-5 s/29 days [32]
FORCE 3×10-6 s/4.3 days
GWIS - 3 filters [33] 1.6×10-6 s/2.2 days [33]
GWIS - 1 filter [33] 3.8×10-7 s/0.5 days [33]
  1. We included the recent GWIS approach that is described as ‘exhaustive’, but uses filtering to avoid computing test statistics for all pairs of SNPs.