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!
You can turn it into a data.frame using the generic function as.data.frame.
Thank you! Is there any option in ChIPseeker to write overlapped genes?
Your question is unclear, but take a look at addFlankGeneInfo parameter
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) 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.
You can use intersect() function to get overlapping genes/peaks.
Annotating your peak and saving into your_peakAnno varable:
your_peakAnno <- annotatePeak(files[], 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")
nanog_annot <- as.data.frame(peakAnnoList[["Nanog"]]@anno)
pou5f1_annot <- as.data.frame(peakAnnoList[["Pou5f1"]]@anno)
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