Following read mapping, methylation levels were estimated on a per CpG basis by taking the fraction of reads containing methylated non-bisulfite-converted C nucleotides over the sum of all reads mapping to a given CpG, and multiplying this fraction by 100 (ie, CpG percent methylation=(count C)/(count C+count T) × 100). All processing of CpG read count files, sample quality control, and initial statistical analyses were carried out using the package methylKit (Akalin et al, 2012b), implemented in R v3.0 (www.R-project.org).
