How to get output of annotated genes from ChIPseeker tool
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26 days ago
EES ▴ 20

Hi,

I am new at ChIP-Seq analysis. I used ChIPseeker package through R but I couldn't figure out how to get output of annoteted genes. Please help me!

Thank you.

ChIPseeker peakannotation • 320 views
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You can turn it into a data.frame using the generic function as.data.frame.

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Thank you! Is there any option in ChIPseeker to write overlapped genes?

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Your question is unclear, but take a look at addFlankGeneInfo parameter

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Hi,

I already used that option as following:

peakAnnoList <- lapply(samplefiles, annotatePeak, TxDb=txdb, 
                       tssRegion=c(-1000, 1000), verbose=FALSE)

when I draw plots using;

genes= lapply(peakAnnoList, function(i) as.data.frame(i)$geneId)
vennplot(genes)

vennplot.peakfile(samplefiles)

vennplot(genes) finds 611 common genes between samplefiles and vennplot.peakfile(samplefiles) finds 674 peaks.

But when I check the output files I can not find same number common genes and peaks.

So that I want to write output of this common genes and peaks used at vennplot.

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Hi EES,

You can use intersect() function to get overlapping genes/peaks.

e.g.

intersect(genes$A, genes$B)
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