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

[Arnaud Amzallag, Ph.D]

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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