I have a matrix of Beta values for 700K+ CpG sites in a from 129 samples in DNA methylation dataset. Using Zuguang Gu's ComplexHeatmap package, I've created a heatmap of the top 1000 M-values with greatest median absolute deviation. Rows of the heatmap are CpG sites, and columns are samples.
We have identified an interesting subset of CpGs, shown in the top horiztonal box (outlined in black) in the image below. I am interested in whether there is a way to identify which CpG sites are included in this box. I have searched for a way to extract information about ComplexHeatmap clusters, but I've come up empty handed. I can add row names to my heatmap, but there are so many CpGs included that it is impossible to read the names.
Does anyone have experience with this or have ideas how this could be done?
Thank you very much!
