[BioC] Making use of the Apis mellifera assembly 2 data in goSeq

[Hervé Pagès]

On 02/27/2012 02:02 PM, Corby, Vanessa wrote:
> Argh.  This is what I was afraid of...

Why not try to make yours? See the makeOrgPackageFromNCBI() function in
AnnotationDbi:

   library(AnnotationDbi)
   ?makeOrgPackageFromNCBI

(Would be nice if the goseq documentation could mention this.)

If you run into problems while trying to use makeOrgPackageFromNCBI()
to roll up your own org.Am.eg.db package, please come back with a
precise description of the problem. Thanks!

Cheers,
H.

>
> Vanessa
>
> -----Original Message-----
> From: Hervé Pagès [mailto:hpages at fhcrc.org]
> Sent: Monday, February 27, 2012 2:51 PM
> To: Corby, Vanessa
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Making use of the Apis mellifera assembly 2 data in goSeq
>
> Vanessa,
>
> On 02/27/2012 12:04 PM, Corby, Vanessa wrote:
>> Page 3 of the goseq documentation states
>>
>> "In order to link GO categories to genes, goseq uses the organism packages from Bioconductor.
>> These packages are named org.<Genome>.<ID>.db, where<Genome>   is a
>> short string identifying the genome and<ID>   is a short string
>> identifying the gene identi_er. Currently, goseq will automatically
>> retrieve the mapping between GO categories and genes from the relevant package (as long as it is installed) for commonly used genome/ID combinations."
>>
>> Let's say I want to use the organism package for the Apis mellifera version 2 genome, a supported genome according to the goseq supportedGenomes() command.  I see that there are several packages that follow the naming convention org.<Genome>.<ID>.db, but none of these is for the Apis version 2 genome.  What organism package do I install for Apis mellifera 2?  Can I use BSgenome.Amellifera.UCSC.apiMel2 even though it does not follow the proper naming scheme?
>
> The org.<Genome>.<ID>.db packages contain annotations (more precisely mappings between gene ids and other kinds of ids). The BSgenome.* packages (like Amellifera.UCSC.apiMel2) contain no annotations, only genomes (i.e. DNA sequences). Of course there is no way you can use one to replace an org.<Genome>.<ID>.db package.
>
> Cheers,
> H.
>
> PS: Please use the "Reply" button so emails are grouped by thread. This discussion is already splitted in 3 different threads on the list which is not going to help. Thanks!
>
>>
>> Thanks.
>>
>> Vanessa
>>
>> Research Molecular Biologist
>> USDA-ARS
>> Carl Hayden Bee Research Center
>> 2000 E. Allen Rd., Tucson, AZ  85719
>>
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>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319