Adding gene symbol to generegiontrack in Gviz [R]
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17 months ago
ksh4718 • 0

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.

R Gviz mm10 • 1.2k views
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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)

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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

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