Table 2.
Average p-values for bipolar methylation detection
| ( 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 | |
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.