[BioC] hyperGTest - GO node universe?

[Seth Falcon]

Hi Edward,

Edward Bolanger <ebolanger at yahoo.com> writes:
> Hi,
>
> I use a set of 1000 yeast genes as the 'universe' for the
> hyperGTest. I then filter the resulting significant GO terms to those
> that have a size count greater than 5.
>
> I now wanted to get the 'universe' of all possible GO nodes/terms for
> my set of 1000 yeast genes. I suppose that this would involve mapping
> all the 1000 genes onto GO, and then selecting only those nodes that
> are associated with more than 5 genes.
>
> Is there any way that I can use hyperGtest to do this? Or is there any
> other method/package you suggest that could help me with this?

I think you can get what you want using the geneIdUniverse accessor on
the result object.

    res = hyperGTest(p)
    GOMap = geneIdUniverse(res)
    has5 = sapply(goMap, function(x) length(x) >= 5)
    GOUni = names(GOMap[has5])

All of the accessors for the result object(s) are documented at:
   help("HyperGResult-accessors")

Hope that helps.

+ seth

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