Skip to main content

Table 5 Parameters and results of scheme c simulation

From: A robust and efficient statistical method for genetic association studies using case and control samples from multiple cohorts

Pop.

p

q

D

f 1

f 2

f 3

p ^ ± s . d .

Method 1*

Method 1**

Method 3

χ2 ± s.d.

ρ (%)

χ2 ± s.d.

ρ (%)

χ2 ± s.d.

ρ (%)

1

0.5

0.5

0

0.1

0.05

0

0.50 ± 0.02

2.0 ± 6.1

2

1.9 ± 2.9

0

0.9 ± 1.3

0

2

0.3

0.7

0

0.1

0.05

0

0.30 ± 0.02

2.2 ± 5.9

2.1

1.8 ± 2.9

0.2

1.0 ± 1.3

0

3

0.7

0.3

0

0.2

0.1

0

0.70 ± 0.02

1.5 ± 3.9

0.5

2.0 ± 2.8

0

1.0 ± 1.3

0

4

0.5

0.5

0.15

0.2

0.1

0

0.48 ± 0.02

57.8 ± 21.8

99.2

52.5 ± 19.0

98

24.1 ± 9.2

79.1

5

0.5

0.5

0.1

0.1

0

0

0.49 ± 0.02

74.5 ± 24.1

99.7

68.7 ± 20.9

99.6

35.0 ± 11.0

97.7

6

0.5

0.5

0.05

0.1

0

0

0.50 ± 0.02

20.0 ± 12.3

42.6

19.6 ± 11.9

41.5

9.3 ± 5.8

11.8

7

0.3

0.7

0.07

0.3

0.1

0

0.29 ± 0.02

16.4 ± 12.7

32.4

14.2 ± 10.9

25

6.5 ± 4.9

4.5

8

0.3

0.7

0.05

0.3

0.1

0

0.29 ± 0.02

9.5 ± 8.9

12.6

8.2 ± 7.7

8.8

3.7 ± 3.6

1

9

0.7

0.3

-0.07

0.1

0

0

0.70 ± 0.02

102.6 ± 29.7

100

93.5 ± 26.1

99.9

44.7 ± 12.0

99.6

10

0.7

0.3

-0.05

0.1

0

0

0.70 ± 0.02

53.7 ± 21.1

96.6

50.5 ± 19.3

96.2

24.0 ± 9.0

80.1

  1. Means and standard deviations (s.d.) of estimates of empirical statistical power (ρ) and the test statistic based on 200 cases and 200 controls from 1000 repeated computer simulations. The left panel lists values of the simulation parameters and the right the estimates. ρ is estimated as proportion (%) of significant tests at the Bonferroni threshold 5 × 10-5 in 1000 simulations.
  2. * when the true simulated parameters were used in the association test.
  3. ** when the penetrance parameters f 1-3 were constantly set to be (1, ½, 0).