Fig. 1
Workflow for pwrEWAS. From an existing tissue-type-specific data set, J CpG-specific means and variances are estimated. Next, P CpGs are sampled with replacement from the collection of CpGs. For two groups, the mean of one group is changed by Δβ, while the mean of the other group remains unchanged. Δβ comes from a truncated normal distribution N(0, τ2). These parameters are then used to simulate β-values for the two groups. A CpG with an absolute difference in mean methylation greater than a predefined detection limit (default: 0.01) is considered as truly differentially methylated. Next, the simulated data set is used to test for differential, comparing the mean methylation signatures between the two groups. A CpG is defined as “detected” if its corresponding FDR is smaller than a predefined threshold (default: 0.05). Each CpG can fall into one of six categories described in Table 1. The marginal power is calculated as the proportion of True Positives among all truly differentially methylated CpGs