hey everyone, I'm performing ChIP-Seq analysis using diffbind, after doing:

dba.count(peaksets, summits=250)

I would like to get the binding affinity Matrix into a text file.

help will be highly appriciated!!

counts <- dba.peakset(myDBA, bRetrieve=TRUE, writeFile="myFile.csv")

You will get back the normalized count scores; you can get raw read counts by changing the value for the score parameter in dba.count().