[BioC] wrong format in GOTERM

[Seth Falcon]

On 24 Jun 2005, fhong at salk.edu wrote:

> Dear list;
>
> I am using package GO and try to extract goterm for some genes.
>> mget("GO:0008372", GOTERM)
>
>> From my record, I would get the following output before
>> mget("GO:0008372", GOTERM)
>
> $"GO:0008372"
> GOID = GO:0008372
> Term = cellular_component unknown
> Definition = Used for the annotation of gene products whose
> localization is not known or cannot be inferred.
> Ontology = CC
>
> But I don't know what happened, not it only gives me
>> mget("GO:0008372", GOTERM)
> $"GO:0008372" list() attr(,"GOID") [1] "GO:0008372" attr(,"Term")
> [1] "cellular_component unknown" attr(,"Synonym") [1] NA
> attr(,"Secondary") character(0) attr(,"Definition") [1] "Used for
> the annotation of gene products whose localization is not known or
> cannot be inferred."  attr(,"Ontology") [1] "CC" attr(,"class") [1]
> "GOTerms" attr(,"class")attr(,"package") [1] "annotate"
>
> And I wouldn't extract Term information out from this format, anyone
> can help me to resolve this puzzle?

Try:
library(annotate)

The last line of the output gives the clue:
> "GOTerms" attr(,"class")attr(,"package") [1] "annotate"

Basically, what is stored in the GOTERM environment are instances of
the GOTerms class and this class is defined in the annotate package.
So to get the nice printout, you need annotate loaded.

Hmm, perhaps the GO package should depend on annotate?

+ seth