How do I retrieve consensus peakset?
1
0
Entering edit mode
@eli7javasky-9060
Last seen 6.8 years ago
European Union

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

 

diffbind peakset • 953 views
ADD COMMENT
1
Entering edit mode
Gord Brown ▴ 640
@gord-brown-5664
Last seen 19 months ago
United Kingdom

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 COMMENT
0
Entering edit mode

Thank you so much

ADD REPLY

Login before adding your answer.

Traffic: 247 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6