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 -
1. 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 : 2. 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 Im 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 ?
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 :/