How to get output of annotated genes from ChIPseeker tool

Question

[MS]

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.

[rpolicastro]

You can turn it into a data.frame using the generic function as.data.frame.

[MS]

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

[Aspire]

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

[MS]

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.

[gglim]

Hi EES,

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

e.g.

intersect(genes$A, genes$B)

Answer 1

[kashiff007]

Annotating your peak and saving into your_peakAnno varable:

your_peakAnno <- annotatePeak(files[[7]], tssRegion=c(-2000, 0), TxDb=txdb)

Writing your_peakAnno table into your file:

write.table(as.data.frame(your_peakAnno@anno), file="your_peakAnno.txt", quote = F, row.names = F, sep = "\t")

Answer 2

[CB]

Get annotation data frame

nanog_annot <- as.data.frame(peakAnnoList[["Nanog"]]@anno)
pou5f1_annot <- as.data.frame(peakAnnoList[["Pou5f1"]]@anno)

https://hbctraining.github.io/In-depth-NGS-Data-Analysis-Course/sessionV/lessons/12_annotation_functional_analysis.html