Table 2.

Association Analysis of Hirschsprung's Disease Data.

The Name of Gene	The Number of SNPs	P-values
		Basis of both GVF and β(t)		FPCA Approach		Basis of beta-Smooth Only		Kernel Based Tests
		Rao's Efficient Score Tests		Test Statistics		Rao's Efficient Score Tests		SKAT	SKAT-O
		B-sp Basis	Fourier Basis	Rao	gt	B-sp Basis	Fourier Basis
PROK1	10	0.283	0.553	0.283	0.159	0.283	0.553	0.245	0.262
PROKR1	7	4.23 × 10–2	0.191	4.23 × 10–2	0.386	4.23 × 10–2	0.191	0.298	0.365
PHOX2B	5	0.063	0.069	0.063	0.755	0.063	0.069	0.257	0.265
ASCL1	5	0.882	0.551	0.668	0.170	0.668	0.551	0.565	0.493
HOXB5	6	0.552	0.596	0.552	0.680	0.552	0.596	0.586	0.684
RET	7	8.62 × 10–23	4.81 × 10–23	8.62 × 10–23	2.74 × 10–24	8.62 × 10–23	4.81 × 10–23	2.11 × 10–14	1.96 × 10–18

The results of “Basis of both GVF and β(t)” were based on smoothing both the GVF and the genetic effect function β(t), the results of “FPCA Approach” were based on FPCA approach, and the results of “Basis of beta-Smooth Only” were based on smoothing the genetic effect function β(t) only approach. Abbreviation: gt = global test. The order of B-spline basis was 4, and the number of basis functions of B-spline was K = K_β = 10; the number of Fourier basis functions was K = K_β = 11. In the case of FPCA, the number of knots of linear spline basis was taken as K_β = 10 and the truncation lag K = 20. The p-values which are smaller than 0.05 are marked by boldface.