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Table 2 Summary of performance measures across minor allele frequency combinations, n = 2000

From: Improving machine learning reproducibility in genetic association studies with proportional instance cross validation (PICV)

Measure, Model Scenario Sensitivity, without interaction Sensitivity, with interaction Specificity, without interaction Specificity, with interaction PPV, without interaction PPV, with interaction NPV, without interaction NPV, with interaction
SNP1 MAF: 0.1 3.06e-17 9.89e-08 N.S. N.S. 1.90e-18 7.67e-08 N.S. N.S.
SNP2 MAF: 0.1
SNP1 MAF: 0.2 7.04e-20 4.54e-05 3.88e-02 N.S. 3.68e-11 5.56e-06 4.35e-02 1.89e-02
SNP2 MAF: 0.1
SNP1 MAF: 0.2 1.69e-10 1.69e-10 N.S. 6.87e-03 4.06e-09 4.06e-09 N.S. N.S.
SNP2 MAF: 0.2
SNP1 MAF: 0.3 1.59e-08 2.47e-05 4.35e-02 N.S. 9.27e-09 2.47e-05 3.46e-02 N.S.
SNP2 MAF: 0.1
SNP1 MAF: 0.3 6.14e-04 5.02e-11 N.S. N.S. 3.07e-16 1.22e-14 N.S. N.S.
SNP2 MAF: 0.2
SNP1 MAF: 0.3 5.16e-04 4.33e-04 N.S. N.S. 1.75e-04 1.75e-04 N.S. N.S.
SNP2 MAF: 0.3
SNP1 MAF: 0.4 9.94e-05 7.67e-08 N.S. N.S. 3.52e-08 5.53e-10 N.S. N.S.
SNP2 MAF: 0.1
SNP1 MAF: 0.4 6.65e-17 1.45e-04 N.S. N.S. 5.36e-09 2.42e-02 N.S. N.S.
SNP2 MAF: 0.2
SNP1 MAF: 0.4 2.71e-08 4.54e-05 N.S. N.S. 8.97e-07 4.46e-06 N.S. N.S.
SNP2 MAF: 0.3
SNP1 MAF: 0.4 1.63e-05 1.41e-03 N.S. N.S. 2.66e-03 8.62e-04 N.S. N.S.
SNP2 MAF: 0.4
SNP1 MAF: 0.5 8.97e-07 7.06e-09 N.S. N.S. 2.27e-06 1.27e-07 4.85e-03 N.S.
SNP2 MAF: 0.1
SNP1 MAF: 0.5 9.42e-18 6.75e-05 1.28e-02 N.S. 4.00e-12 8.60e-06 N.S. N.S.
SNP2 MAF: 0.2
SNP1 MAF: 0.5 4.38e-07 2.47e-05 N.S. N.S. 7.67e-08 4.12e-10 N.S. 1.46e-02
SNP2 MAF: 0.3
SNP1 MAF: 0.5 2.69e-07 5.54e-05 N.S. N.S. 7.06e-09 8.62e-04 N.S. N.S.
SNP2 MAF: 0.4
SNP1 MAF: 0.5 1.27e-07 6.92e-06 N.S. 1.54e-02 2.89e-12 9.27e-09 N.S. N.S.
SNP2 MAF: 0.5