DiffBind currently does not support adding labels such as gene names to the differentially bound sites.
As you suggest, the best bet is to export the table, and annotate and plot it using other tools. You can get the full table either using dba.report() with th=1, or use only the differentially bound sites by assigning the return value from the call to dba.plotVolcano(). The relevant fields are the FDR and Fold columns in the table.
This is on my list of possible features to add, but there are a number of things ahead of it! The main thing it requires is an interface to add an annotation to the peakset, as most ChIP peak intervals do not correspond directly to annotated genes.
this is true, although the dogma since the GREAT/bedtools days is the closest gene is the relevant one. Although all the looping data do or do not confirm it.
Thank you Roy for the answer, do you plan to implement an option as such?
This is on my list of possible features to add, but there are a number of things ahead of it! The main thing it requires is an interface to add an annotation to the peakset, as most ChIP peak intervals do not correspond directly to annotated genes.
this is true, although the dogma since the GREAT/bedtools days is the closest gene is the relevant one. Although all the looping data do or do not confirm it.