assess methylation differences in known genomic intervals (enhancers etc) #3
Description
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.