[BioC] Drawing induced GO graphs

[Wolfgang Huber]

Dear Daniel

thank you for your feedback! Would it be possible to

(i) send a code example that we can reproduce (i.e. where the variables 
"test" and "universe" are defined)?

(ii) send the output of sessionInfo() after running the example?

  Best wishes
	Wolfgang

-- 
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Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber


daniel jupiter wrote:
> Hi all,
> 
> undoubtedly this is a silly question.
> After struggling for quite some time, I think I've been able to do
> hypergerometric tests for GO enrichment using hyperGTest.
> The documentation is a bit thin, but it's eventually become clear.
> The next step is to draw the DAG, with significant genes highlighted, and
> term names replacing GO IDs.
> A wrinkle: I am just interested in a particular set of genes, relative to a
> universe - there is no array, no annotation involved.
> 
> In any case, here is my code.
> 
> params <- new("GOHyperGParams", geneIds = test,
> universeGeneIds = universe,annotation="org.Rn.eg.db",
> conditional = FALSE, categoryName="GO", ontology="CC", pvalueCutoff=.01)
> 
> x=hyperGTest(params)
> 
> y=termGraphs(x,use.terms=TRUE , pvalue=.01)
> 
> plotGOTermGraph(y,x, node.colors=c(sig="white",not="blue"),
> node.shape="circle", add.counts=FALSE)
> 
> I am returned the following error:
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "nodes", for signature
> "list"
> 
> Am I doing something obviously wrong?
> 
> Any help is greatly appreciated.
> 
> Thanks
> 
> Dan Jupiter.
>