Hi,

Can anybody using Diffbind help me with this query -

So I am trying to create a consensus peakset from peak calls in Diffbind to analyse it downstream with DESeq2.

The samplesheet h3k4me3.csv looks like this -

SampleID   Tissue   Factor    Condition   Treatment  Replicate   bamReads   bamControl   Peaks   PeakCaller   PeakFormat  ScoreCol  LowerBetter
1          GC       h3k4me3   tumor       none       1           path       path         path    raw          raw         4         FALSE
2          NT       h3k4me3   normal      none       1           path       path         path    raw          raw         4         FALSE
3          GC       h3k4me3   tumor       none       2           path       path         path    raw          raw         4         FALSE
4          NT       h3k4me3   normal      none       2           path       path         path    raw          raw         4         FALSE
5          GC       h3k4me3   tumor       none       3           path       path         path    raw          raw         4         FALSE
6          NT       h3k4me3   normal      none       3           path       path         path    raw          raw         4         FALSE

I want to create a consensus peak of all normal samples where the peak occurs in atleast 2 of 3 of the samples. So I read in the file and ran this command:

h3k4me3_readin <- dba(sampleSheet="h3k4me3.csv")
h3k4me3_consensus <- dba.peakset(h3k4me3_readin, consensus = DBA_CONDITION, minOverlap=0.66)

This created 2 new consensus peaksets - one for normal, the other for tumor.

The problem: I want to create a final consensus peakset from the normal consensus peakset created in step 1 and peaks of sampleID 1. I am not sure how to do this and what I'm trying doesn't seem to give me the right results -

I tried -

h3k4me3_consensus.2 <- dba.peakset(h3k4me3_consensus, consensus = 1:8, minOverlap=0.66)
h3k4me3_consensus.2 <- dba.peakset(h3k4me3_consensus, consensus = c(1,8), minOverlap=0.66)

Does anybody have any suggestions on how to go about this ?

Thanks!

ALTERNATIVELY - Is there an easier way to merge / create consensus peaks ? If so, I'll happily switch!

p.s Asking this here despite having posted it on Bioconductor because I haven't received a reply there and I'm in a rush to figure this out :/