How to get the list of genes from DiffBind dba.report or dba.peakset
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Bordiya • 0
@bordiya-16743
Last seen 3.1 years ago

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!

diffbind • 828 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 11 days ago
CRUK, Cambridge, UK

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.

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Thanks a lot Rory!

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Bordiya • 0
@bordiya-16743
Last seen 3.1 years ago

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

 

 

 

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mdidish • 0
@cbee3b30
Last seen 3 days ago
France

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)
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