Currently, methscan scan finds DMRs and reports their genomic coordinates. To answer specific research questions like "which enhancers are differentially methylated between cell group A and cell group B?" one needs to intersect the DMR coordinates with enhancer coordinates and quantify the degree of overlap, etc.
A more direct approach would be to allow the user to provide a set of intervals to be tested for differential methylation directly, reporting a p-value for each. This would make it straightforward to find e.g. which enhancers are lowly methylated in a specific population of cells.
Currently,
methscan scanfinds DMRs and reports their genomic coordinates. To answer specific research questions like "which enhancers are differentially methylated between cell group A and cell group B?" one needs to intersect the DMR coordinates with enhancer coordinates and quantify the degree of overlap, etc.A more direct approach would be to allow the user to provide a set of intervals to be tested for differential methylation directly, reporting a p-value for each. This would make it straightforward to find e.g. which enhancers are lowly methylated in a specific population of cells.