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Table 2 Number of times interacting alleles were observed as highest scoring model (rank = 1) or second (rank = 2) using PIA 2.0a for 2-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

66

66

50

36

50

83

67

79

 

2

4

4

14

11

14

10

15

6

56

1

55

55

46

33

46

84

58

68

 

2

3

3

10

11

9

2

5

5

57

1

58

58

52

19

52

82

66

78

 

2

7

7

10

12

10

8

7

9

58

1

88

88

76

58

76

96

89

92

 

2

1

1

11

18

11

3

4

5

59

1

50

50

45

36

45

64

48

61

 

2

13

13

13

16

12

10

14

11

  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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