Results of differential methylation analysis of three kidney samples compared to three rectum samples, with and without using SWAN. (a) Percentage of RRBS true positives identified at various q-value significance thresholds. Using the SWAN method (magenta) consistently detects more RRBS true positives than analyzing raw data (black). (b) Receiver operating characteristic (ROC) curve of an analysis using SWAN compared to an analysis of the raw data. Using SWAN (magenta) prior to differential methylation analysis results in performance gains.