[BioC] Gene Ontology relationships

[Seth Falcon]

Hi,

> davidl at unr.nevada.edu writes:
>> Hello Seth,
>>
>>      Thank you very much for the response.  I read the help pages for those
>> functions and they sound like they are exactly what I was looking for.  I ran
>> into a problem actually using termGraphs, however.  This may be something
>> simple and stupid but I am having trouble identifying what the problem is. 
>> This is the relevant part of my workflow and the resulting error message:
>>
>>> paramsFvBup<-new("GOHyperGParams", geneIds=llsupFvB,
>> universeGeneIds=llsUniversFvB, annotation="mouse4302", ontology="BP",
>> pvalueCutoff=0.05, conditional=TRUE, testDirection="over")
>>> FvBupOverBP<-hyperGTest(paramsFvBup)
>>> htmlReport(FvBupOverBP, file="test.html")
>> #That all worked fine and the table looks good
>>> termGraphs(FvBupOverBP,pvalue=0.05, use.terms=TRUE)
>> Error in "names<-"(`*tmp*`, value = c(NA_character_, NA_character_,
>> NA_character_,  :
>>         'value' argument must specify unique names

I believe that I've fixed the problem.  GOstats_2.2.5 is available via
biocLite (not yet for OS X).  In the meantime, I noticed a labeling
problem with plotGOTermGraph and GOstats_2.2.6 will be available in
the next couple of days.

Please let me know if you encounter further problems --- these
functions for extracting subgraphs of the results and plotting are
quite new and somewhat experimental so I'm open to suggestions.

Best,

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org