Question: DiffBind - Difficulties construction appropriate consensus set
0
11 months ago by
Rob Buurstede0 wrote:

Hello,

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,

Best,

Rob

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