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Question: How do I retrieve consensus peakset?
0
gravatar for eli7javasky
3.0 years ago by
European Union
eli7javasky0 wrote:

Hi,

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 = 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,

Elisheva J

 

ADD COMMENTlink modified 3.0 years ago by Gord Brown580 • written 3.0 years ago by eli7javasky0
1
gravatar for Gord Brown
3.0 years ago by
Gord Brown580
United Kingdom
Gord Brown580 wrote:

Hi,

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 "dba.report", 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).

Cheers,

 - Gord

ADD COMMENTlink written 3.0 years ago by Gord Brown580

Thank you so much

ADD REPLYlink written 3.0 years ago by eli7javasky0
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