Question: How to show the fraction of peaks in CDS regions using ChIPseeker
0
gravatar for tianf
3.2 years ago by
tianf0
tianf0 wrote:

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 • 593 views
ADD COMMENTlink modified 3.2 years ago by Guangchuang Yu1.1k • written 3.2 years ago by tianf0
Answer: How to show the fraction of peaks in CDS regions using ChIPseeker
0
gravatar for Guangchuang Yu
3.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
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.
ADD COMMENTlink written 3.2 years ago by Guangchuang Yu1.1k
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