Question: Adding gene symbol to generegiontrack in Gviz [R]
0
gravatar for ksh4718
6 months ago by
ksh47180
ksh47180 wrote:

Hello. I am trying to create a GeneRegionTrack for Gviz, using the mm10 genome. I can't seem to display the gene symbol rather than the Ensembl transcript ID in the gene track. I've tried changing the transcription annotation to gene and symbol but neither work. Please see below:

library(Gviz)
library(GenomicRanges)
library(Mus.musculus)

chr <- 'chr11'
gen <- 'mm10'

txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene

grtrack <- GeneRegionTrack(txdb, genome = gen,
                           chromosome = chr, name = "UCSC known genes",
                           transcriptAnnotation='symbol')
plotTracks(grtrack, chromosome=11,from=102885336, to=102899200)

This is the output

If I change symbol to gene:

grtrack <- GeneRegionTrack(txdb, genome = gen,
                           chromosome = chr, name = "UCSC known genes",
                           transcriptAnnotation='gene')
plotTracks(grtrack, chromosome=11,from=102885336, to=102899200)

This is the new output

I want the transcript IDs to be replaced with the gene symbol. A side note that this works fine with the human genome, but not the mouse. I'm not sure why.

mm10 gviz R • 416 views
ADD COMMENTlink modified 6 weeks ago by maxklap0 • written 6 months ago by ksh47180

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

ADD REPLYlink written 6 months ago by RamRS30k

I'm having the same issue and haven't been able to figure it out. I just posted an issue to the Gviz github, so hopefully there's a useful response there soon. https://github.com/ivanek/Gviz/issues/36

ADD REPLYlink written 6 weeks ago by maxklap0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1795 users visited in the last hour