BMC Bioinformatics

Table 3 Type I error rates and power† for mixed resource study designs.

From: Haplotype association analyses in resources of mixed structure using Monte Carlo testing

		CC	TRIO	ASP	LP1	LP2
		EC	PC	PC	EC	EC	TRIOCC	ASPCC	LP1CC	LP2CC
	Total sample size	1,000*	1,500†	1,000	1,500	1,000	2,500	2,000	2,500	2,000
	pedigree-informed null	NA	0.044	0.051	0.049	0.054	0.051	0.039	0.042	0.044
	pedigree-naive null	0.058	0.048	0.061	0.062	0.054	0.053	0.046	0.048	0.060
Freq risk hap	GRR
0.17	2.0	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000
	1.5	0.910	0.846	0.914	0.970	0.900	0.996	0.998	0.996	0.998
	1.35	0.672	0.634	0.650	0.786	0.632	0.904	0.912	0.934	0.918
	1.2	0.280	0.290	0.264	0.358	0.254	0.516	0.518	0.566	0.500
0.10	2.0	0.994	0.994	1.000	1.000	1.000	1.000	1.000	1.000	1.000
	1.5	0.754	0.722	0.732	0.896	0.762	0.950	0.960	0.984	0.978
	1.35	0.456	0.434	0.406	0.604	0.448	0.744	0.730	0.804	0.788
	1.2	0.210	0.166	0.238	0.256	0.186	0.324	0.390	0.372	0.358
0.07	2.0	0.990	0.968	0.994	1.000	0.998	1.000	1.000	1.000	1.000
	1.5	0.642	0.586	0.646	0.820	0.688	0.866	0.904	0.952	0.944
	1.35	0.399	0.312	0.400	0.554	0.368	0.598	0.674	0.752	0.678
	1.2	0.168	0.161	0.151	0.252	0.146	0.250	0.264	0.336	0.294
0.04	2.0	0.855	0.798	0.886	0.992	0.928	0.981	0.990	0.998	0.998
	1.5	0.363	0.348	0.378	0.624	0.474	0.618	0.616	0.746	0.726
	1.35	0.245	0.184	0.236	0.304	0.241	0.340	0.411	0.430	0.429
	1.2	0.096	0.152	0.114	0.152	0.118	0.240	0.167	0.200	0.176

Results from most powerful statistic for each single resource analyses and mixed resource analyses. All controls within LP1 and LP2 are familial controls.
* = 500 cases, 500 controls
† = 500 cases, 1,000 controls
† Power is shown for the hapMC with the pedigree-informed MLE estimation
NA = pedigree informed phasing not applicable to case-control null.

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