Question: How do I retrieve consensus peakset?
gravatar for eli7javasky
2.5 years ago by
European Union
eli7javasky0 wrote:


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[1]))
mod = dba.count(mod)
mod = dba.contrast(mod, categories=DBA_CONDITION, minMembers=2)
mod = dba.analyze(mod, method=DBA_DESEQ2)
report =, 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,

Elisheva J


ADD COMMENTlink modified 2.5 years ago by Gord Brown570 • written 2.5 years ago by eli7javasky0
gravatar for Gord Brown
2.5 years ago by
Gord Brown570
United Kingdom
Gord Brown570 wrote:


The consensus peakset is constructed when you call "dba.count".  You can retrieve it using "dba.peakset" with  "bRetrieve=TRUE" as a parameter, or when you call "", give a threshold of 1.0, like so: "th=1.0" to indicate that you want all peaks (i.e. everything with a pvalue of 1.0 or less, which is everything).


 - Gord

ADD COMMENTlink written 2.5 years ago by Gord Brown570

Thank you so much

ADD REPLYlink written 2.5 years ago by eli7javasky0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 151 users visited in the last hour