Nonparametric Bayesian clustering to detect bipolar methylated genomic loci

Wu, Xiaowei; Sun, Ming-an; Zhu, Hongxiao; Xie, Hehuang

doi:10.1186/s12859-014-0439-2

BMC Bioinformatics

Table 2 Average p-values for bipolar methylation detection

From: Nonparametric Bayesian clustering to detect bipolar methylated genomic loci

( i , j )	δ						δ
	0.2	0.25	0.3	0.35	0.4		0.2	0.25	0.3	0.35	0.4
(1, 1)	1	1	1	1	1	(3, 7)	0.03	0.02	0.02	0.01	0.02
(1, 2)	1	1	1	1	1	(3, 8)	0.02	0.01	0.01	0.01	0.02
(1, 3)	0.95	0.90	0.95	0.99	0.97	(3, 9)	0.01	0.01	0.01	0.01	0.01
(1, 4)	0.82	0.71	0.76	0.76	0.81	(3,10)	0	0	0	0.01	0
(1, 5)	0.58	0.69	0.73	0.70	0.64	(3,11)	0	0	0	0	0
(1, 6)	0.51	0.47	0.58	0.50	0.57	(3,12)	0	0	0	0	0
(1, 7)	0.46	0.34	0.29	0.42	0.36	(3,13)	0	0	0	0	0
(1, 8)	0.23	0.29	0.25	0.27	0.35	(4, 4)	0.05	0.04	0.03	0.03	0.04
(1, 9)	0.14	0.14	0.15	0.15	0.16	(4, 5)	0.02	0.02	0.01	0.02	0.01
(1,10)	0.09	0.09	0.11	0.08	0.09	(4, 6)	0.01	0.01	0.01	0.01	0.01
(1,11)	0.07	0.07	0.06	0.06	0.07	(4, 7)	0	0	0	0	0
(1,12)	0.05	0.04	0.05	0.05	0.05	(4, 8)	0	0	0	0	0
(1,13)	0.02	0.02	0.03	0.03	0.04	(4, 9)	0	0	0	0	0
(1,14)	0	0	0	0	0	(4,10)	0	0	0	0	0
(1,15)	0	0	0	0	0	(4,11)	0	0	0	0	0
(2, 2)	0.72	0.79	0.81	0.60	0.61	(4,12)	0	0	0	0	0
(2, 3)	0.56	0.59	0.48	0.41	0.44	(5, 5)	0	0	0	0	0
(2, 4)	0.38	0.41	0.45	0.28	0.28	(5, 6)	0	0	0	0	0
(2, 5)	0.23	0.20	0.24	0.16	0.15	(5, 7)	0	0	0	0	0
(2, 6)	0.14	0.13	0.10	0.11	0.07	(5, 8)	0	0	0	0	0
(2, 7)	0.06	0.08	0.07	0.05	0.06	(5, 9)	0	0	0	0	0
(2, 8)	0.05	0.05	0.05	0.04	0.04	(5,10)	0	0	0	0	0
(2, 9)	0.03	0.03	0.03	0.04	0.03	(5,11)	0	0	0	0	0
(2,10)	0.03	0.03	0.03	0.02	0.02	(6, 6)	0	0	0	0	0
(2,11)	0.02	0.01	0.02	0.01	0.02	(6, 7)	0	0	0	0	0
(2,12)	0	0.01	0.01	0.01	0.01	(6, 8)	0	0	0	0	0
(2,13)	0	0	0	0	0	(6, 9)	0	0	0	0	0
(2,14)	0	0	0	0	0	(6,10)	0	0	0	0	0
(3, 3)	0.23	0.31	0.11	0.16	0.15	(7, 7)	0	0	0	0	0
(3, 4)	0.16	0.12	0.08	0.08	0.10	(7, 8)	0	0	0	0	0
(3, 5)	0.06	0.04	0.05	0.05	0.04	(7, 9)	0	0	0	0	0
(3, 6)	0.04	0.03	0.03	0.03	0.04	(8, 8)	0	0	0	0	0

The average p-values are calculated from 100 simulations for a 4-CpG segment with 16 reads, using τ= 0.32 and different δ values. Significant p-values (under significance level 0.05) are marked with boldfaced font. Zero-valued p-values are actually <5 × 10^-3. In each simulation, we generate i reads with methylation pattern (0,0,0,0), j reads with methylation pattern (1,1,1,1), and randomly generate (16-i-j) reads with other methylation patterns.

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