Hi all,

I am analyzing H2AZ ChIP seq data. I have the dba.report and dba.peakset which give chromosome number and peak position of differential peaks. I would like to get list of genes corresponding to those peaks. How can I do this?

Thank you!

There are a number of annotation packages available that can work on the GRanges object returned by dba.report() or a bed file. Within Bioconductor, ChIPpeakAnno is popular -- many DiffBind users feed the results into ChIPpeakAnno.

I used ChIPpeakAnno in combination with other packages, please find the script in the link below. It works great!!

Three years after, if someone has the same question, here is a proposition with ChIPseeker:

library(ChIPseeker)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
library(org.Mm.eg.db)

peak.counted <- dba.count(peak.dba, summits=T, score = DBA_SCORE_SUMMIT_POS)
# retrieve summit list (GRanges object)
summits <- dba.peakset(kdm6b.counted, bRetrieve=TRUE)
# annotate with ChIPseeker
peak.anno = annotatePeak(
  peak = summits,
  tssRegion = c(-1000, 1000),
  TxDb = TxDb.Mmusculus.UCSC.mm10.knownGene,
  annoDb = "org.Mm.eg.db"
)
plotAnnoPie(peak.anno)
dfPA = as.data.frame(peak.anno)