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Table 1 Success rates for identification of interaction pairs of SNPs from simulation studies

From: Detecting gene-gene interactions using a permutation-based random forest method

  

Interaction SNP Pair Detection Success Rate

  

Sample Size = 2000

Sample Size = 4000

SNP Numbers

Heritability

Highest EDM

Lowest EDM

Highest EDM

Lowest EDM

5

0.001

52 %

7 %

70 %

16 %

5

0.005

99 %

28 %

100 %

43 %

5

0.01

100 %

34 %

100 %

68 %

5

0.05

100 %

100 %

100 %

100 %

5

0.1

100 %

100 %

100 %

100 %

5

0.2

100 %

100 %

100 %

100 %

5

0.3

100 %

100 %

100 %

100 %

5

0.4

100 %

100 %

100 %

100 %

10

0.001

8 %

3 %

29 %

1 %

10

0.005

80 %

4 %

99 %

13 %

10

0.01

100 %

8 %

100 %

43 %

10

0.05

100 %

98 %

100 %

100 %

10

0.1

100 %

100 %

100 %

100 %

10

0.2

100 %

100 %

100 %

100 %

10

0.3

100 %

100 %

100 %

100 %

10

0.4

100 %

100 %

100 %

100 %

15

0.001

6 %

0 %

8 %

0 %

15

0.005

51 %

2 %

77 %

6 %

15

0.01

93 %

4 %

100 %

12 %

15

0.05

100 %

92 %

100 %

100 %

15

0.1

100 %

100 %

100 %

100 %

15

0.2

100 %

100 %

100 %

100 %

15

0.3

100 %

100 %

100 %

100 %

15

0.4

100 %

100 %

100 %

100 %

20

0.001

0 %

0 %

2 %

1 %

20

0.005

10 %

2 %

39 %

3 %

20

0.01

49 %

0 %

93 %

12 %

20

0.05

100 %

70 %

100 %

98 %

20

0.1

100 %

100 %

100 %

100 %

20

0.2

100 %

100 %

100 %

100 %

20

0.3

100 %

100 %

100 %

100 %

20

0.4

100 %

100 %

100 %

100 %

25

0.001

1 %

0 %

1 %

0 %

25

0.005

2 %

0 %

10 %

1 %

25

0.01

15 %

1 %

44 %

2 %

25

0.05

99 %

30 %

100 %

87 %

25

0.1

100 %

87 %

100 %

100 %

25

0.2

100 %

99 %

100 %

100 %

25

0.3

100 %

100 %

100 %

100 %

25

0.4

100 %

100 %

100 %

100 %

  1. Success rates for identification of interaction pairs of SNPs with different numbers of SNPs, heritabilities, models with highest/lowest EDMs, under the sample sizes of 2000 or 4000 with balanced cases and controls. The success rates were calculated using 100 replicate datasets. The percentage was calculated as the fraction of correctly detection times of the interacting SNP pair, M0P0 and M1P1, in 100 replicate datasets under each genetic constraint combination of number of SNPs (5, 10, 15, 20 or 25), heritability (0.001, 0.005, 0.01, 0.05, 0.1, 0.2, 0.3 or 0.4), extreme EDM (highest or lowest) and sample size (2000 or 4000)