does anyone of you have recommendations for inter-multisample DMR (differentially methylated region) calling. I have WGBS methylation data for multiple cell populations and want to identify DMR specific for any group of them. For example DMRs specific for Lung and Heart in difference to Skin + DMR specific for Lung in difference to Heart and Skin + DMR specific to Heart in difference to Skin and Lung. For more populations you obviously get more comparisons. Now are most DMR callers only for pairwise comparisons. DSS-general and RadMeth offer group wise comparisons which seems nice but would need all pair-wise groupings and especially always includes all samples. Are there any alternatives?
Alternatively, we are currently doing all pairwise comparisons, then try and merge overlapping DMR and later reassociate the DMR generated this way to different cell types (currently via kmeans but looking into other things). Unfortunatly, I have to assume to lose information that way when a DMR is part specific to one cell type and part specific to multiple cell types. If anyone has suggestions or solved similar problems I'd love to hear some input?