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Table 2 Average p-values for bipolar methylation detection

From: Nonparametric Bayesian clustering to detect bipolar methylated genomic loci

( i , j ) δ ( i , j ) 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
  1. 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.