after regressing out the top five principal components to remove variations due to batch effects and biological factors. We then selected the top 1% variable CpGs to call the VMRs for each brain region using the regionFinder3 function of bsseq and VMRs, retaining VMRs with more than five CpGs for further analysis. We estimated the DNA methylation level of each VMR by the total number of reads supporting methylated cytosine divided by the total number of reads supporting either methylated or unmethylated cytosine in the region.
