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Question: How to display gene symbols in UCSC Track in Gviz
0
gravatar for Greg G.
19 months ago by
Greg G.0
USA/Seattle
Greg G.0 wrote:

Hello everyone,

I am trying to get Gviz::UcscTrack to display HGNC symbols, or at least the default name from the gene() function. The piece of code I am using is pasted below. Any help is highly appreciated.

 

ucscGenes <- UcscTrack(genome="hg38", table="ncbiRefSeq", track = 'NCBI RefSeq', trackType="GeneRegionTrack", 
                                   chromosome="chr19", rstarts = "exonStarts", rends = "exonEnds", 
                                   gene = "name", symbol = 'name', transcript = "name", 
                                   strand = "strand", stacking = 'pack', showID = T, geneSymbol = T)

 

Thank you

 

ADD COMMENTlink modified 19 months ago by James W. MacDonald48k • written 19 months ago by Greg G.0
1
gravatar for James W. MacDonald
19 months ago by
United States
James W. MacDonald48k wrote:

The UCSC tables in general don't have the HUGO symbols, so you end up having to add those yourself. But it's really easy to do.

> ucscGenes <- UcscTrack(genome="hg38", table="ncbiRefSeq", track = 'NCBI RefSeq', trackType="GeneRegionTrack",
                                   chromosome="chr19", rstarts = "exonStarts", rends = "exonEnds",
                                   gene = "name", symbol = 'name', transcript = "name",
                                   strand = "strand", stacking = 'pack', showID = T, geneSymbol = T)

> z <- ranges(ucscGenes)

> library(org.Hs.eg.db)

> mcols(z)$symbol <- mapIds(org.Hs.eg.db, gsub("\\.[1-9]$", "", mcols(z)$symbol), "SYMBOL","REFSEQ")
> ucscGenes2 <- ucscGenes
> ranges(ucscGenes2) <- z

> plotTracks(list(ucscGenes, ucscGenes2), chromosome = "chr19", from = 1e6, to = 1.4e6, transcriptAnnotation = "symbol")
ADD COMMENTlink written 19 months ago by James W. MacDonald48k

Fantastic! It worked like a charm. I suppose with the mapping method I can assign any form of nomenclature to the genes. Right?

Thanks,
Greg

ADD REPLYlink written 19 months ago by Greg G.0

I don't know what you mean by 'with the mapping method I can assign any form of nomenclature to the genes'. Can you clarify?

ADD REPLYlink written 19 months ago by James W. MacDonald48k

It's OK. I meant the mapIds() function. Thanks again.

ADD REPLYlink written 19 months ago by Greg G.0
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