Table 2.

Type I error levels and power for collapsing with minor allele frequency < 0.01 for both non-synonymous and gene-based variants.

Variants	Method	Type I error	Avg. power	Min power
Non-synonymous	aSum	0.12	(0.19)	(1.00)
	C-α	0.07	0.13	0.90
	CAST	0.06	0.11	0.93
	CMAT	0.05	0.10	1.00
	CMC	0.10	(0.16)	(0.93)
	FPCA	0.05	0.05	0.57
	KBAC	0.03	0.06	0.77
	PWST	0.50	(0.58)	(1.00)
	RC	0.07	0.12	0.93
	RVT1	0.05	0.11	0.77
	RVT2	0.06	0.12	0.93
	SKAT	0.08	(0.12)	(0.93)
	SKAT-O	0.10	(0.16)	(0.93)
	VT	0.07	0.04	0.70
	WSS	0.05	0.11	0.90
Gene-based	aSum	0.12	(0.15)	(1.00)
	C-α	0.06	0.10	0.91
	CAST	0.06	0.09	0.97
	CMAT	0.12	(0.16)	(1.00)
	CMC	0.11	(0.20)	(0.97)
	FPCA	0.05	0.07	0.82
	KBAC	0.04	0.06	0.88
	PWST	0.65	(0.85)	(1.00)
	RC	0.08	(0.13)	(0.94)
	RVT1	0.06	0.10	0.91
	RVT2	0.05	0.11	0.85
	SKAT	0.08	(0.11)	(0.97)
	SKAT-O	0.10	(0.14)	(1.00)
	VT	0.06	0.04	0.85
	WSS	0.12	(0.17)	(0.94)

Type I error levels and average (avg) power were averaged over 200 replicates. Minimal (min) power is the proportion of replicates for which at least one associated region of interest was detected. Power is given in parenthesis if the type I error was inflated.

aSum, adaptive summation; CAST, cohort allelic sum test; CMAT, cumulative minor-allele test; CMC, combined multivariate cluster; FPCA, functional principal component analysis; KBAC, kernel-based adaptive cluster; PWST, p-value weighted sum test; RC, RARECOVER; RVT, rare variant test 1 and 2; SKAT, sequencing kernel association test; SKAT-O, optimal unified SKAT; VT, variable threshold; WSS, weighted sum statistic.