Question: how to retrieve binding affinity matrix in diffbind
gravatar for hamaor
9 months ago by
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!!

chip-seq dba.count diffbind • 484 views
ADD COMMENTlink modified 8 months ago by Rory Stark550 • written 9 months ago by hamaor0
gravatar for iamjli
9 months ago by
iamjli10 wrote:

For completeness, this question has been answered here.

ADD COMMENTlink written 9 months ago by iamjli10
gravatar for Rory Stark
8 months ago by
Rory Stark550
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark550 wrote:
dba.peakset(myDBA, bRetrieve=TRUE, writeFile="BindingAffinityMatrix.csv")

The values will be the score used in dba.count(), the default is DBA_SCORE_TMM_MINUS_FULL (TMM normalised read counts after subtracting control reads, based on the number of reads in each bam file). To get, for example, raw read counts, use DBA_SCORE_READS. See help page for dba.count(). You can change the score without recounting:

myDBA <- dba.count(myDBA, peaks=NULL, score=DBA_SCORE_xxx)
ADD COMMENTlink written 8 months ago by Rory Stark550
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