[BioC] Problem with hgu133plus2.db package
mtmorgan at fhcrc.org
Tue Jun 16 17:27:08 CEST 2009
Hi Morten --
Morten Hansen wrote:
> Hi Martin
> Yes - my package is using a namespace.
> Everything worked fine after adding your suggestions to the DESCRIPTION and NAMESPACE files.
> I need all the info in the hgu133plus2GO2PROBE - I think...
I don't know what the function does, but I was supposing that you were
going to look at only a subset of the GO ids in the table, and then
perhaps you would subset the map using [, and perhaps mappedLkeys or the
like to extract information
Basically, thinking that you only want a subset of the available
information, and that it would pay to get only the information you want.
> Which function from AnnotationDbi can you suggest to extract information with?
> Br - Morten
> Fra: Martin Morgan [mtmorgan at fhcrc.org]
> Sendt: 16. juni 2009 13:41
> Til: Morten Hansen
> Cc: bioconductor at stat.math.ethz.ch
> Emne: Re: [BioC] Problem with hgu133plus2.db package
> Hi Morten --
> Does your package have a namespace? Maybe you need to have
> Imports: AnnotationDbi
> in the DESCRIPTION file and
> importMethodsFrom(AnnotationDbi, as.list)
> in the NAMESPACE file. But is this really what you want to do? Maybe
> it's better to use the standard AnnotationDbi interface to extract just
> the information you're interested in, instead of making everything into
> a list?
> Morten Hansen wrote:
>> I have a problem with the hgu133plus2.db package.
>> Usually when I want to use the data from hgu133plus2GO2PROBE , I do the following:
>>> a <- as.list( hgu133plus2GO2PROBE )
>> Works fine.
>> Now I am making a package and need to do the same. When running a function inside the package that does the same as above I get the following error:
>> Error in as.list.default(hgu133plus2GO2PROBE) :
>> no method for coercing this S4 class to a vector
>> I also tried using mappedkeys() as explained in the example in help, but I get the same error.
>> I have tested it on a clean R and Bioconductor installation.
>> Any suggestions?
>> My sessionInfo():
>> R version 2.9.0 (2009-04-17)
>> attached base packages:
>>  stats graphics grDevices utils datasets methods base
>> other attached packages:
>>  icmmUtils_1.0.0 biomaRt_2.0.0 hgu133plus2.db_2.2.11 annotate_1.22.0 annaffy_1.16.0 KEGG.db_2.2.11
>>  GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.6.0 Biobase_2.4.1
>> loaded via a namespace (and not attached):
>>  RCurl_0.98-1 XML_2.5-1 xtable_1.5-5
>> Br - Morten Hansen
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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