[BioC] ref : org.Hs.eg.db

Steve Lianoglou lianoglou.steve at gene.com
Thu Nov 21 22:24:55 CET 2013


On Thu, Nov 21, 2013 at 1:07 PM, Abhishek Pratap <apratap at sagebase.org> wrote:
> just in case it was missed earlier..still trying to see if org.Hs.eg.db
> could be used to find all the coding and non-coding genes.

Have you tried monkeying around with it at all? There may be a super
elegant way to do so, but you should also be able to cobble your own
solution together in a number of ways.

(1) Looking at the output from `cols(org.Hs.eg.db)` suggest that there
is at least one column (UNIPROT) that can tell you protein info about

(2) Another thing to think about is that you can query a TranscriptDb
object to get coding exons only. Assuming you have the `Homo.sapiens`
package, you can query the TxDb package that comes with it to get all
the coding exons (`cdsBy`) for example then link transcript IDs to
entrez ids in a number of ways.


Steve Lianoglou
Computational Biologist

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