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

[Hervé Pagès]

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
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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