[BioC] question about Gviz

[Hahne, Florian]

Well, the main culprit here is really the TranscriptDB package. It does
not seem to deal at all with gene symbols, so there is no way for Gviz to
automatically fetch those. If you come up with a way to match the UCSC
gene identifiers back to gene symbols you could stick those into the
GeneRegionTrack using the 'symbol' replacement method. E.g.,
symbol(foo) <- mappingTable[match(transcript(foo), mappingTable$UCSCId),])
I am not sure how this mapping is supposed to be done in the Bioconductor
world these days. You may be able to find a way using one of the org.db
packages. Or maybe you will have to download a mapping table directly from
the UCSC table browser.
With the next release of Bioconductor (or already now if you are working
with the devel branch), Gviz supports building tracks from a whole range
of standard annotation files. You could then export the whole known.gene
table from UCSC as a GTF file and import in again as a GeneRegionTrack
object. Alternatively you may want to look into the BiomartGeneRegionTrack
class which will fetch the gene models from Ensembl, but this includes the
HUGO gene symbols.
Florian


-- 






On 2/7/13 10:51 AM, "Bogdan Tanasa" <tanasa at gmail.com> wrote:

>Dear all,
>
>I am using the following code below in order to retrieve the gene
>annotations in Gviz package :
>please could advise on what shall I modify in order to display the HUGO
>gene symbol on each gene ? thanks !
>
>library("GenomicFeatures")
>hg18db <- makeTranscriptDbFromUCSC(genome = "hg18",tablename =
>"knownGene")
>saveDb(hg18db, file="hg18db_knownGene.sqlite")
>txdb <-loadDb("hg18db_knownGene.sqlite")
>txTr <-
>GeneRegionTrack(txdb,genome="hg18",chromosome="chr9",showId=TRUE,geneSymbo
>l=TRUE,name="UCSC")
>plotTracks(txTr,from=start,to=end)
>
>-- bogdan
>------------------
>
>	[[alternative HTML version deleted]]
>
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