[BioC] In the TranscriptDb object, where do the Entrez Gene IDs come from ?

[Marc Carlson]

Hi Arnaud,

I am glad that you like this feature.   The ultimate source of this
information is by linking the known gene table to the knownToLocusLink
table at UCSC.

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=184855093&hgta_doSchemaDb=hg19&hgta_doSchemaTable=knownToLocusLink


  Marc



On 01/26/2011 01:31 PM, Arnaud Amzallag, Ph.D wrote:
> Hello, 
>
> I have been trying on the UCSC table browser to find a table that links kgIDs with gene IDs, but I did not find that. With the package GenomicFeatures, when constructing a TranscriptDB object from UCSC, one can group the transcripts by gene, the gene names being the Entrez gene IDs, which is quite neat.
>
>   
>> txdb <- makeTranscriptDbFromUCSC(genome = "hg18", tablename = "knownGene")
>> txbygene <- transcriptsBy(txdb, by="gene")
>> head(names(txbygene))
>>     
> [1] "1"         "10"        "100"       "1000"      "10000"     "100009676"
>
> I would like to know how the the kgID have been associated with Entrez gene IDs.
>
> Thanks !
>
> Arnaud
>
>
>
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