4.3.5. Correlation Analysis and DMR Detection

A correlation analysis was carried out based on Pearson's coefficient [94]. DSS software was used to identify DMRs and differentially methylated loci between WT and RT samples [95–97]. Information from neighboring cytosine sites (i.e., spatial correlation) and site read depths were analyzed to improve the accuracy of long cytosine reads. Variance among biological replicates was analyzed using a beta-binomial distribution model. DMRs were annotated, and DMR-related genes were defined as those having coding regions (from the transcriptional start site (TSS) to the transcriptional end site (TES)) or promoter regions (i.e., upstream 2-kb from the TSS) that overlapped with the distribution of DMRs.
