Table 1 Average computation time (in seconds) for 500 trios and 500, 1000, 1500, or 2000 population controls.

From: Conditioning adaptive combination of P-values method to analyze case-parent trios with or without population controls

No. of population controls

rvTDT

pedgene

SKAT a

ADA b

conADA(PC) c

conADA(PC) d

500

15.68

4.15

27.60

62.52

76.50

486.64

1000

15.36

6.04

39.61

81.27

78.58

490.72

1500

15.31

8.53

2.51

99.48

73.43

487.79

2000

15.21

11.82

3.25

116.09

77.12

492.15

  1. aAccording to the default of the SKAT package, a small sample adjustment is applied when the total sample size is <2000. Therefore, in addition to 500 cases contributed by 500 trios, when the number of population controls is <1500, the total sample size is <2000 and SKAT required more time.
  2. bThe P-values of ADA were obtained with 1,000 permutations.
  3. cThe P-values of conADA were obtained with the sequential Monte Carlo permutation29, and the minimum and maximum numbers of permutations were set as 10 and 1000, respectively.
  4. dThe P-values of conADA were obtained with the sequential Monte Carlo permutation29, and the minimum and maximum numbers of permutations were set as 100 and 10,000, respectively.
Back to article page