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


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

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.

b Simulated data sets were described previously [14] and were obtained from Dr. Moore by request.

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.

Mechanic et al. BMC Bioinformatics 2008 9:146   doi:10.1186/1471-2105-9-146