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.

-- 
Daniel C. Jupiter, Ph.D.
Postdoctoral Research Associate
Department of Systems Biology and Translational Medicine
College of Medicine
Texas A&M Health Science Center
702 SW H.K. Dodgen Loop
Temple, TX 76504

979.997.2106 | Fax 254.742.7145
djupiter@tamu.edu | www.tamhsc.edu

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