Hello,

I wanted to know, is it somehow possible to annotate the MA plot of only promoter peaks? I know DiffBind doesn't have built in annotation functionality, but has someone attempted to do this kind of graphs?

I can imagine, that one needs to extract the DBA object as granges, then annotate the binding regions, then manually plot it. But is there any other good workarounds? Is it even possible the way I mentioned? I am just a biologist trying to do analysis, therefore, my skills are limited :(

Many thanks for your help!

For example(I made it in photoshop)

You've got the required workflow about right.

Another simpler option is to use the set of promoter regions as the consensus peakset (passed using the peaks= parameter to dba.count), then run the analysis only on promoter regions.