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Table 3 Standard and variance tests capture different signals in simulations

From: X-inactivation informs variance-based testing for X-linked association of a quantitative trait

Simulation parameters

X-inactivation and 10% additional noise in heterozygous females

X-inactivation and 20% additional noise in heterozygous females

Standard

Variance

Shared (expected)

Standard

Variance

Shared (expected)

N = 1000

MAF = 0.1

a = 0.1

26.5

17.8

4.5 (4.7)

26.9

40.6

10.6 (10.9)

N = 1000

MAF = 0.3

a = 0.1

51.0

29.2

15.1 (14.9)

49.9

62.5

30.8 (31.2)

N = 1000

MAF = 0.1

a = 0.2

73.8

24.0

18.0 (17.7)

73.6

47.5

34.6 (34.9)

N = 1000

MAF = 0.3

a = 0.2

98.1

39.2

37.7 (38.5)

97.8

71.2

63.6 (69.6)

N = 2000

MAF = 0.1

a = 0.1

46.7

29.6

14.2 (13.8)

45.9

65.9

29.8 (30.2)

N = 2000

MAF = 0.3

a = 0.1

81.1

45.2

36.9 (36.7)

80.8

87.2

70.5 (70.5)

N = 2000

MAF = 0.1

a = 0.2

95.7

41.4

39.7 (39.6)

95.2

75.8

72.2 (72.2)

N = 3000

MAF = 0.1

a = 0.1

62.3

39.4

25.4 (24.5)

62.5

82.2

51.5 (51.4)

N = 3000

MAF = 0.3

a = 0.1

93.1

57.9

54.1 (53.9)

93.1

96.0

89.3 (89.4)

N = 3000

MAF = 0.1

a = 0.2

99.3

54.8

53.6 (54.4)

99.2

89.7

88.9 (89.0)

N = 5000

MAF = 0.1

a = 0.1

83.5

57.0

47.6 (47.6)

82.3

95.7

78.7 (78.7)

  1. Shown are percentages of simulations where the test in the column positively identifies the QTL with p-value < 0.05. The shared column denotes the case where both the standard and the variance test significantly identify the QTL, and the differences between the shared and the two tests indicate the different signals the two tests capture. The expected is calculated by assuming the standard and variance tests are independent. Simulation scenarios include varying sample sizes (N), minor allele frequencies of the QTL (MAF), and effect sizes of the QTL (a).