Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis

Grange, Laura; Bureau, Jean-François; Nikolayeva, Iryna; Paul, Richard; Van Steen, Kristel; Schwikowski, Benno; Sakuntabhai, Anavaj

doi:10.1186/s12863-015-0174-3

Table 9 Power and family-wise error rate (FWER) of FORCE, MBMDR, Plink Epistasis and Plink FastEpistasis on 6 epistasis models with or without noise

From: Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis

				Model 1	Model 2	Model 3	Model 4	Model 5	Model 6
No noise	FORCE		Power^a	1	0.97	0.96	1	0.93	0.99
	FORCE		FWER^b	0.05	0.02	0.02	0.06	0.05	0.04
	MBMDR		Power	1	1	1	0.98	0.87	0.97
	MBMDR		FWER	0.02	0	0	0.01	0.01	0.01
	Plink	Epistasis	Power	0	1	0.32	0.98	0.9	0.97
		Epistasis	FWER	0.04	0.05	0.02	0.02	0	0.03
		FastEpistasis	Power	0	1	0.38	0.98	0.81	0.84
		FastEpistasis	FWER	0.07	0.07	0.02	0.02	0.01	0.05
GE	FORCE		Power	0.99	0.99	0.97	1	0.95	0.99
	FORCE		FWER	0.03	0.03	0.08	0.03	0.03	0.04
	MBMDR		Power	1	1	1	0.99	0.85	1
	MBMDR		FWER	0	0	0.01	0.02	0	0
	Plink	Epistasis	Power	0	1	0.28	0.99	0.87	0.99
		Epistasis	FWER	0	0	0.07	0.02	0	0
		FastEpistasis	Power	0.01	1	0.31	1	0.74	0.92
		FastEpistasis	FWER	0.04	0	0.09	0.05	0	0
MS	FORCE		Power	0.99	0.96	0.95	1	0.93	0.99
	FORCE		FWER	0.07	0.02	0.02	0.03	0.03	0.06
	MBMDR		Power	1	1	1	0.99	0.8	0.94
	MBMDR		FWER	0	0	0	0	0	0
	Plink	Epistasis	Power	0	1	0.26	1	0.8	0.97
		Epistasis	FWER	0.03	0.02	0.08	0.02	0	0
		FastEpistasis	Power	0	1	0.29	1	0.67	0.91
		FastEpistasis	FWER	0.06	0.01	0.1	0.04	0	0
PC	FORCE		Power	0.08	0.55	0.13	0.33	0.23	0.37
	FORCE		FWER	0.03	0.05	0.05	0.06	0.04	0.07
	MBMDR		Power	0.72	0.98	0.12	0.09	0.11	0.16
	MBMDR		FWER	0	0	0	0	0	0
	Plink	Epistasis	Power	0	0.95	0.01	0.21	0.19	0.28
		Epistasis	FWER	0.04	0.03	0.05	0.06	0.01	0
		FastEpistasis	Power	0	0.99	0.01	0.23	0.07	0.21
		FastEpistasis	FWER	0.07	0.03	0.04	0.06	0.01	0.01

Genotype errors (GE), missing data (MS) or phenocopy (PC). ^aIn bold, power higher than 50%. ^bIn bold, FWER lower than 5%.

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