MEDIPS.exportWIG - I see that while there is an option of exporting
counts, it looks like these are the raw counts instead of the EdgeR normalized counts. Is there a way to get the normalized counts instead? Currently the closest I can get to this is by using rpkm in the
format parameter, however this is suboptimal as there are differences between these two normalization units, especially given that I used
diff.method="edgeR" to identify DMRs.
Also note, I am familiar with the fact that deeptools can generate bigwig directly from the BAM, and while they provide a number of normalization methods with their
bamCoverage function, I would still prefer to use the normalized counts from edgeR present in MEDIPS if possible.
Any advice is welcomed!