[BioC] GO analysis code snippet

J.Oosting at lumc.nl J.Oosting at lumc.nl
Tue Jul 31 10:03:43 CEST 2007

> I am looking for some GO analysis code-snippet for the following task,
> 1) list all the GO terms under "molecular function"
You could use the GOMFOFFSPRING environment from the GO package. See the
example in the help.
> 2) For a given GO id, list the associated Entrez gene IDs (or
> probe IDs for U133A)
The metadata packages generally do this. For EntrezGene id mapping you
can use the humanLLMappings package, for the Affymetrix U133A the
hgu133a2 package.

> A further question: is there a package analyzeing GO hierarchically? I
> mean,
> testing the parent nodes first; if it is not significant, then,
> the
> children? I think most of the packages just test all the GO terms
> simutanuously.
The globaltest package has functionality to use the structure of the
GO-graph to limit the number of tests. You should take a look at chapter
4 of the vignette for an example.


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