Question: how to retrieve binding affinity matrix in diffbind
0
gravatar for hamaor
3 months ago by
hamaor0
hamaor0 wrote:

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!!

diffbind dba.count • 125 views
ADD COMMENTlink modified 3 months ago by Rory Stark2.8k • written 3 months ago by hamaor0
Answer: how to retrieve binding affinity matrix in diffbind
1
gravatar for Rory Stark
3 months ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k wrote:
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().

ADD COMMENTlink written 3 months ago by Rory Stark2.8k
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