[BioC] GOLOCUSID

[Marc Carlson]

Hi John,

Saroj is correct in that you should find the mappings you seek in the
appropriate organism package ("org.Xx.eg.db" where "Xx" is the initial
of the genus and species of the organism you are studying).  You
probably want to look at the GO2ALLEGS mapping.

  Marc



Saroj K Mohapatra wrote:
> Hi John:
>
> I do not have a general answer. However, the "org." packages do have a mapping from GO to Entrez gene. For example, there is the mouse package org.Mm.eg.db that has org.Mm.egGO which maps between the two identifiers.
>   
>> library("org.Mm.eg.db")
>> ?org.Mm.egGO2EG
>>     
>
> -----------
>      org.Mm.egGO is an R object that provides mappings between entrez
>      gene identifiers and the GO identifiers that they are  directly
>      associated with. This mapping and its reverse mapping do NOT
>      associate the child terms from the GO ontology with the gene. 
>      Only the directly evidenced terms are represented here.
> -----------
>
> You could use the appropriate org package for your species.
>
> Hope this helps,
>
> Saroj
>
> ----- Original Message -----
> From: "John Lande" <john.lande77 at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern
> Subject: [BioC] GOLOCUSID
>
> dear Bioc,
>
> I have retrieved an old stript to extract genes associated with a specific
> GO term from a previous release of BioC.
>
> it exploited the enviroment GOLOCUSID form the package GO.
>
> thei enviroment is no longer available in the current release bioc 2.3.
> is there an equivalent enviroment in some other package?
>
> how can I retrieve the genes associated with a specific go term in bioc now.
>
> thank you
>
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>
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