The methylation level for each C in the CG, CHG and CHH sequence context was summed in adjacent 10-kb windows over all autosomal chromosomes. Non-CG DNA methylation profiles were determined by adding mCHG and mCHH profiles. Clustering was performed based on the Pearson correlation over all 10-kb windows transformed into a distance measure (as 1 – Pearson correlation) and using the hclust R function. Data for smoothing of non-CG mC on chromosome 10 were retrieved as for the clustering. In addition, smoothing with cubic splines was determined before plotting using the smooth. spline R function with spar argument set to 0.3.
