Fig. 2: Accuracy analysis per CpG site on control mixture dataset 1.

a Violin plots showing the predicted methylation frequencies (y axis) for each control mixture set with a given proportion of methylated reads (x axis). The Pearson’s correlation (r), coefficient of determination (r²), and root mean square error (RMSE) are given for each tool. b For each method, we indicate the proportion of sites predicted outside a 10% window around the expected methylation proportion, i.e., each predicted site in the m% dataset was classified as “outside” if its predicted percentage methylation was outside the interval [(m − 5)%, (m + 5)%] for intermediate methylation values, or outside the intervals [0,5%] or [95%, 100%] for the fully unmethylated or fully methylated sets, respectively. The percentage is indicated on top of each bar, except for 100%. c Empirical cumulative distribution function (ECDF) plot showing the number of true negatives (y axis) for each tool according to different thresholds for the predicted methylation frequency below which a site was called unmethylated (x axis), using the dataset of 100 fully unmethylated sites. d ECDF plot showing the number of true positives (y axis) for each tool according to different thresholds for the predicted methylation frequency above which a site was called fully methylated (x axis), using the dataset of 100 fully methylated sites.