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Table 3 Number of times interacting alleles were observed as highest (rank = 1) or second highest (rank = 2) pairs in the top 10 triplets using PIA 2.0a for 3-SNP interactions using balanced simulated data sets

From: Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions

  

Scoring Function

 

Model Numberb

Rank

%Correct

Sensitivity +Specificity

PPV+NPV

Risk Ratio

Odds Ratio

Gini Index

Probability Difference

Total (Overall)c

55

1

73

73

79

58

79

81

67

63

 

2

9

9

5

9

5

7

15

12

56

1

61

61

62

50

62

79

51

68

 

2

10

10

6

8

6

6

10

8

57

1

72

72

71

47

71

78

55

75

 

2

7

7

10

12

10

8

15

7

58

1

92

92

90

85

90

96

86

92

 

2

3

3

2

4

2

2

4

3

59

1

57

57

55

52

55

61

42

60

 

2

10

10

10

8

10

10

9

10

  1. a Data were generated using cell counts to assign case versus control status (IFRACT = 0) and excluded the training data when scoring and running 10 10-fold cross-validations for functions 1–5 (ITRAIN = 0, FRACT = 0.1, NTIME = 10). Results including training data in scoring are presented in Additional file 1, Table S1.
  2. b Simulated data sets were described previously [14] and were obtained from Dr. Moore by request.
  3. c Total score is the summation over all scoring functions after linearly scaling the score for each individual function such that the top score is 50.0.
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BMC Bioinformatics

ISSN: 1471-2105

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