[BioC] entrez gene to genome coordinates

[Marc Carlson]

Hi Guarav,

It might be overkill, but you could also use the GenomicFeatures package
to get similar information in a different (GRanges) form.  This
information could come from whatever UCSC Genome browser track you
specified BUT: you would have to be careful to choose a track that used
Entrez Gene IDs as the gene accessions.

So for example this would get you the mouse data:

library(GenomicFeatures)
txdb2 <- makeTranscriptDbFromUCSC(genome="mm9", tablename="knownGene")
result = exonsBy(txdb2,by="gene")
head(result)


  Marc



On 08/06/2010 09:17 AM, Bhatti, Gaurav wrote:
> Hey
> I am looking for genome locations for a list of entrez ids. I have used org.Hs.db in the past. However there are several ids in my list which do not have annotation in the database. What are other packages available? Are there other tables I can download from NCBI to get the annotation my self?
>
> Gaurav
>
>
>
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