Question: DiffBind - Difficulties construction appropriate consensus set
gravatar for Rob Buurstede
11 months ago by
Rob Buurstede0 wrote:


I am new to the field of bioinformatics and currently using your R package (DiffBind_2.6.6) for the analysis of my ATAC-seq data to identify differences in chromatin accessibility between groups. Due to the nature of the project I want to construct a specific consensus set to use for dba.count, but I am struggling to achieve this. Your help/advice would be much appreciated.

In the consensus peakset I would like to include:

       - the peaks that are present in at least 6 out of 7 control samples (regardless of the experimental group)

       - the peaks in at least 4 out of 8 experimental samples (regardless of the control group)

Is there an easy way to construct a consensus peakset meeting the requirements stated above?


As I couldn't figure out how to construct a consensus peakset as such, I constructed two separate consensus peaksets (one for each of the requirement using the code below), but I have not yet succeeded in merging these to use them in dba.count.

control_consensus <- dba.peakset(control, minOverlap = 6)
consensus_peaks_control <- dba.peakset(control_consensus, control_consensus$masks$Consensus, bRetrieve = TRUE)

exp_consensus <- dba.peakset(exp, minOverlap = 4)
consensus_peaks_exp <- dba.peakset(exp_consensus, exp_consensus$masks$Consensus, bRetrieve = TRUE)

If a more direct method is not available, how would you advice to combine these two separate peaksets for further use?

Thank you very much,



diffbind • 153 views
ADD COMMENTlink written 11 months ago by Rob Buurstede0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 365 users visited in the last hour