Question

How to show the fraction of peaks in CDS regions using ChIPseeker

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tianf • 0

@tianf-10989

Last seen 8.1 years ago

I followed the tutorial of ChIPseeker. But I found that the CDS information could not be shown duing Visualize Genomic Annotation.

http://bioconductor.org/packages/3.3/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#visualize-genomic-annotation

library("ChIPseeker")

files <- getSampleFiles()

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

plotAnnoPie(peakAnno)

How could I show the fraction of peaks in CDS regions as well in the figure?

chipseeker • 1.5k views

ADD COMMENT • link updated 8.1 years ago by Guangchuang Yu ★ 1.2k • written 8.1 years ago by tianf • 0

score 0 · Answer 1 · 2016-10-20

CDS is very general, it contains UTR, extron, intron and some of the promoter (flanking sequence of TSS). If you want to get exactly CDS ratio, you can downgrade promoter in genomic annotation by passing the following parameter to annotatePeak. genomicAnnotationPriority = c("5UTR", "3UTR", "Exon", "Intron", "Promoter", "Downstream", "Intergenic") Then you can sum 5UTR, 3UTR, Exon and Intron as CDS.