Table 2.
Friedman test for effect of LD and MAF on the variable importance of functional SNPs
| Effect | Condition | RF Gini |
RF MDA |
GBM |
GBM + subsetting |
GBM + PCVs |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| x2 | P | x2 | P | x2 | P | x2 | p | x2 | p | ||
| MAF | ρ = 0.9 | 11.9 | 2.6 × 10−3 | 7.0 | 3.0 × 10−2 | 1.7 | 4.2 × 10−1 | 0.6 | 7.5 × 10−1 | 21.5 | 2.1 × 10−5 |
| ρ = 0.5 | 13.8 | 1.0 × 10−3 | 7.0 | 3.0 × 10−2 | 7.9 | 1.9 × 10−2 | 2.3 | 3.1 × 10−1 | 21.8 | 1.9 × 10−5 | |
| ρ = 0.0 | 14.6 | 6.8 × 10−4 | 13.3 | 1.3 × 10−3 | 1.1 | 5.7 × 10−1 | 1.5 | 4.7 × 10−1 | 44.2 | 2.5 × 10−10 | |
| LD | m = 0.1 | 17.6 | 1.5 × 10−4 | 1.0 | 6.1 × 10−1 | 17.7 | 1.4 × 10−4 | 1.4 | 5.0 × 10−1 | 0.5 | 7.8 × 10−1 |
| m = 0.3 | 32.0 | 1.1 × 10−7 | 0.5 | 8.0 × 10−1 | 17.7 | 1.4 × 10−4 | 6.5 | 3.9 × 10−2 | 0.7 | 6.9 × 10−1 | |
| m = 0.5 | 12.7 | 1.7 × 10−3 | 5.0 | 8.2 × 10−2 | 19.6 | 5.6 × 10−5 | 0.3 | 8.4 × 10−1 | 4.5 | 1.0 × 10−1 | |
Tests are performed for the simple effect of MAF at a given LD ρ, and for the simple effect of LD at a given MAF m. All tests have df= 2. With Bonferroni corrections for family-wise α= 0.05, P-values <1.7 × 10−2 indicate significant effects.