Using the posterior distribution of deviance to measure evidence of association for rare susceptibility variants

Lorenzo-Bermejo, Justo; Beckmann, Lars; Chang-Claude, Jenny; Fischer, Christine

doi:10.1186/1753-6561-5-S9-S38

BMC Proceedings

Table 2 Probability values, proportions of positive deviance differences, and power comparisons based on the 200 replicates

From: Using the posterior distribution of deviance to measure evidence of association for rare susceptibility variants

Variant	Effect on Q1	MAF (%)	Probability value						Positive deviance differences (%)						P _W	P _0.1	P _0.05	P _0.01
			Median	2.5th	97.5th	<0.1 (%)	<0.05 (%)	<0.01 (%)	Median	2.5th	97.5th	<0.1 (%)	<0.05 (%)	<0.01 (%)
1			0.26	0.04	0.94	0.100	0.035	0.000	0.08	0.05	0.59	0.540	0.010	0.000				–
2	0.56	0.22	0.35	0.00	0.81	0.205	0.120	0.050	0.43	0.04	0.57	0.045	0.045	0.010	0.0002	<0.0001	0.01095	0.0402
3	–	0.07	0.25	0.05	0.57	0.280	0.015	0.000	0.34	0.02	0.48	0.480	0.315	0.000	<0.0001	<0.0001	<0.0001	–
4	–	0.07	0.26	0.08	0.49	0.100	0.000	0.000	0.09	0.03	0.47	0.510	0.280	0.000	<0.0001	<0.0001	<0.0001	–
5	0.58	0.07	0.22	0.07	0.50	0.180	0.000	0.000	0.08	0.03	0.45	0.615	0.350	0.000	<0.0001	<0.0001	<0.0001	–
6	0.47	0.07	0.56	0.04	0.66	0.200	0.155	0.000	0.40	0.01	0.49	0.330	0.255	0.000	<0.0001	0.00462	0.01861	–
7	1.08	0.07	0.03	0.01	0.80	0.705	0.650	0.115	0.01	0.00	0.50	0.690	0.690	0.485	<0.0001	0.82766	0.45667	<0.0001
8	0.14	16.50	0.18	0.00	0.95	0.345	0.255	0.095	0.40	0.06	0.58	0.065	0.020	0.000	<0.0001	<0.0001	<0.0001	<0.0001
9	0.62	0.07	0.68	0.03	0.79	0.060	0.040	0.005	0.44	0.02	0.51	0.055	0.055	0.020	<0.0001	1	0.63826	0.36808
10	–	0.14	0.26	0.04	0.94	0.100	0.035	0.000	0.08	0.05	0.59	0.540	0.010	0.000	<0.0001	<0.0001	0.17747	–
11	0.30	2.08	0.30	0.00	0.94	0.285	0.195	0.040	0.45	0.07	0.58	0.040	0.020	0.005	0.00106	<0.0001	<0.0001	0.04308
12	0.30	0.07	0.26	0.08	0.49	0.225	0.000	0.000	0.10	0.03	0.47	0.515	0.360	0.000	<0.0001	<0.0001	<0.0001	–
13	0.94	0.07	0.03	0.01	0.80	0.705	0.650	0.115	0.01	0.00	0.50	0.690	0.690	0.475	<0.0001	0.82766	0.45667	<0.0001
14	0.42	0.22	0.26	0.01	0.99	0.140	0.060	0.045	0.43	0.01	0.59	0.050	0.035	0.025	0.36355	0.00374	0.34708	0.41439
15	–	0.07	0.69	0.03	0.75	0.095	0.040	0.000	0.44	0.01	0.51	0.095	0.095	0.020	<0.0001	1	0.04627	0.13167
16	–	0.07	0.67	0.01	0.78	0.325	0.235	0.000	0.42	0.00	0.51	0.320	0.320	0.155	<0.0001	1	0.07399	<0.0001
Any rare variant			0.11	0.00	0.91	0.490	0.395	0.205	0.33	0.01	0.57	0.165	0.095	0.025	<0.0001	<0.0001	<0.0001	<0.0001

MAF is the minor allele frequency. 2.5th and 97.5th are percentiles. P_W is the probability value from a Wilcoxon rank sum test on the null location shift. P_0.1 is the probability value from a two-sample test for equality of proportions (percentage of probability values smaller than 0.1 and percentage of proportions of deviance differences under 0.1); the same applies to P_0.05 and P_0.01.

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ISSN: 1753-6561

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