Table 3 Performance of SAMC on extreme p-values

From: Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests

Site

Parametric p-value

Perm. p-value

CI

SAMC, N = 105

SAMC, N = 106

cg00123214

2.601 ⋅ 10−08

12 ⋅ 10−09

(6.201, 20.962) ⋅ 10−09

6.301 ⋅ 10−09

13.71 ⋅ 10−09

cg00044796

3.779 ⋅ 10−13

4 ⋅ 10−09

(1.090, 10.242) ⋅ 10−09

6.092 ⋅ 10−09

5.065 ⋅ 10−09

cg01821635

3.941 ⋅ 10−18

2 ⋅ 10−09

(0.242, 7.225) ⋅ 10−09

4.500 ⋅ 10−09

6.504 ⋅ 10−09

cg06784218

5.756 ⋅ 10−21

4 ⋅ 10−09

(1.090, 10.242) ⋅ 10−09

2.327 ⋅ 10−09

6.484 ⋅ 10−09

cg08963013

4.625 ⋅ 10−26

6 ⋅ 10−09

(2.202, 13.059) ⋅ 10−09

3.339 ⋅ 10−09

5.460 ⋅ 10−09

cg14252149

5.005 ⋅ 10−34

4 ⋅ 10−09

(1.090, 10.242) ⋅ 10−09

3.358 ⋅ 10−09

5.131 ⋅ 10−09

cg00071950

5.678 ⋅ 10−36

5 ⋅ 10−09

(1.623, 11.668) ⋅ 10−09

8.149 ⋅ 10−09

7.440 ⋅ 10−09

cg02002194

9.238 ⋅ 10−42

4 ⋅ 10−09

(1.090, 10.242) ⋅ 10−09

6.420 ⋅ 10−09

7.501 ⋅ 10−09

cg11266682

1.873 ⋅ 10−46

7 ⋅ 10−09

(2.814, 14.423) ⋅ 10−09

12.62 ⋅ 10−09

6.251 ⋅ 10−09

cg15296535

8.427 ⋅ 10−51

9 ⋅ 10−09

(4.115, 17.085) ⋅ 10−09

6.839 ⋅ 10−09

9.045 ⋅ 10−09

  1. For 10 selected sites, we show the parametric p-value, as calculated by GCTA; the permutation p-value, as calculated by 109 permutations, and the CIs implied by it; and the p-values estimated by SAMC, using N = 105 or N = 106 permutations (with t0 = 1000). SAMC estimates, even for N = 105, appear accurate for all sites, as they lie within the CI calculated from the permutation test
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