[BioC] HyperGTest and genelists

[davidl at unr.nevada.edu]

Hello everyone,

      I like that the new HyperGTest function lets you specify the gene
universe, get only the more specific GO terms in your results, and easily
output a report with the expected counts, actual counts, and p values.  With
the old GOHyperG results, I had written a function that retrieved the list of
significant GOterms, found the gene names associated with those GO terms, and
found the intersection of those gene names and my genes of interest.
So my question is this:

    Is there a way to get the gene names of the genes of interest which were
associated with the over or under represented GO terms found with HyperGTest? 
I noticed there is a function for the GOHyperGResult object (geneIdUniverse)
which retrieves the entrez gene identifiers from your gene universe for all the
tested GO terms.  Is there a way to get only the entrez gene identifiers from
your genes-of-interest group?  Could you then filter out the GO terms which did
not meet the p-value cutoff?  Is there a function which could be applied to
this list to change those entrez identifiers into gene names?  Or is there an
easier way to get the names of the genes from your genes of interest which
contributed to the "Count" column of the html report?  For example, if there
was a method for retrieving the GO terms which met the p-value cutoff from the
GOHyperGResult object, I could just use the function I've already written. 
Thank you very much in advance for whatever help you can provide.  I really
like the new hypergeometric function, and I hope this can be figured out.

Thank you,
Dave