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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

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