Differential methylation between groups of samples was determined at both the probe and region levels (1000 bp regions) to ensure both statistical significance and biological relevance as previously described [60]. At the probe level, a modified t-statistic was computed for each probe corresponding to probe log-ratio differences between CPA and control groups using the ‘limma’ package [101] of Bioconductor [102]. Then, region-level methylation differences were calculated as enrichment of large positive or negative t-statistic values among the probes in each 1000 bp region partition of the loci tiled with probes using the Wilcoxon rank-sum test. A probe and the containing region were called differentially methylated if the p-value of the probe t-statistic was at most 0.05 (uncorrected for multiple testing), log2-fold change between the groups was at least 0.25, and the false discovery rates (FDR) of the region-level statistic was at most 0.2. False positives due to multiple testing are than controlled using the FDR [103] using the method of Benjamini and Hochberg [104].
