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Figure 4 | Genome Biology

Figure 4

From: BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

Figure 4

Coverage probabilities stratified by CpG island status and true methylation level. Coverage probabilities (frequency in which the true value is within a predefined credible interval) at the 95% level are shown for the 75% of bins with the largest depth in the truth (cutoff was 33 reads) for Batman (orange), BayMeth ignoring SssI control information (light red) and BayMeth (red). Three different types of credible intervals (quantile-based, Wald and HPD) are shown for BayMeth, while for Batman and the SssI-free version of BayMeth only quantile-based intervals are available. MEDIPS and BALM do not return any uncertainty estimates. The nominal coverage value is indicated (black dashed line) as a reference. Genomic regions were stratified by CpG density using the threshold of 12.46, which separates CpG islands from non-CpG islands; compare Additional file 2: Figure S1. Further stratification by the true methylation level as derived from WGBS [40] is provided. HPD, highest posterior density; WGBS, whole genome bisulfite sequencing.

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