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Table 3 Number of SNPs and clumps in simulation study 2 with empirical power > 0

From: r2VIM: A new variable selection method for random forests in genome-wide association studies

      

Causal clumps

FP clumps

OR

n

Method

Factor

Total

Causal

no

no SNPs

no

no SNPs

1.3

6000

LR

 

765

9

9

741

2

24

1.3

6000

r2VIM

1

194

8

9

178

13

16

1.3

6000

r2VIM

3

110

8

9

106

3

4

1.3

6000

r2VIM

5

78

8

9

77

1

1

1.1

20000

LR

 

106

5

5

105

1

1

1.1

20000

r2VIM

1

104

5

8

62

32

42

1.1

20000

r2VIM

3

43

4

7

30

8

13

1.1

20000

r2VIM

5

26

4

7

21

3

5

  1. Shown are results for logistic regression (LR) and r2VIM. Columns denote odds ratio (OR), sample size (n), method, factor for r2VIM, total number of SNPs, number of causal SNPs, number of clumps based on causal SNPs, number of SNPs in clumps based on causal SNPs, number of clumps based on false-positive (FP) SNPs and number of SNPs clumps based on false-positive (FP) SNPs