I have been using diffBind to analyze chip-seq data. From what I understand, diffBind creates a consensus peakset from all of the peaks given as input. I have the diffBind report which gives me the differentially bound regions but I would like to see the consensus peakset that diffBind uses. Here is my code:
mod = dba(sampleSheet=paste0(args)) mod = dba.count(mod) mod = dba.contrast(mod, categories=DBA_CONDITION, minMembers=2) mod = dba.analyze(mod, method=DBA_DESEQ2) report = dba.report(mod, method=DBA_DESEQ2, file="report", DataType=DBA_DATA_FRAME)
I am unsure where exactly in the analysis the peakset is created and how to access it.
Thank you so much,