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

BMC Bioinformatics

Table 2 Type I error rates and power† for all data sets and statistics.

		CC*	TRIO^#			ASP*			LP1^#		LP2*
			EC	PC	TDT	EC	PC	TDT	EC	PC	EC	PC
	pedigree-informed null	NA	0.046	0.044	0.045	0.052	0.051	0.051	0.049	0.047	0.054	0.054
	pedigree-naïve null	0.058	0.056	0.048	0.055	0.061	0.061	0.058	0.062	0.047	0.054	0.056
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	1.000	1.000
	1.5	0.910	0.840	0.846	0.846	0.904	0.914	0.916	0.970	0.974	0.900	0.892
	1.35	0.672	0.620	0.634	0.624	0.640	0.650	0.660	0.786	0.778	0.632	0.616
	1.2	0.280	0.276	0.290	0.282	0.256	0.264	0.264	0.358	0.364	0.254	0.268
0.10	2.0	0.994	0.994	0.994	0.994	1.000	1.000	1.000	1.000	1.000	1.000	1.000
	1.5	0.754	0.712	0.722	0.726	0.728	0.732	0.738	0.896	0.900	0.762	0.742
	1.35	0.456	0.422	0.434	0.428	0.378	0.406	0.408	0.604	0.572	0.448	0.428
	1.2	0.210	0.162	0.166	0.170	0.218	0.238	0.242	0.256	0.262	0.186	0.166
0.07	2.0	0.990	0.966	0.968	0.966	0.994	0.994	0.992	1.000	1.000	0.998	0.996
	1.5	0.642	0.574	0.586	0.596	0.620	0.646	0.642	0.820	0.822	0.688	0.666
	1.35	0.399	0.300	0.312	0.312	0.368	0.400	0.396	0.554	0.538	0.368	0.360
	1.2	0.168	0.146	0.161	0.166	0.143	0.151	0.154	0.252	0.252	0.146	0.140
0.04	2.0	0.855	0.777	0.798	0.794	0.867	0.886	0.880	0.992	0.986	0.928	0.920
	1.5	0.363	0.323	0.348	0.338	0.343	0.378	0.376	0.624	0.610	0.474	0.464
	1.35	0.245	0.158	0.184	0.174	0.196	0.236	0.230	0.304	0.317	0.241	0.211
	1.2	0.096	0.139	0.152	0.141	0.087	0.114	0.104	0.152	0.128	0.118	0.112

P-values between (0.036, 0.0635) for 1000 replicates are consistent with a valid 0.05 type 1 error rate.
EC = Explicit controls, PC = pseudocontrols, TDT = transmission disequilibrium test
* = 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.

ISSN: 1471-2105