[BioC] GOstats and KEGG

[Seth Falcon]

Hi Morten and other Category/GOstats users,

Morten Mattingsdal <mortenm at inbox.com> writes:
> But when I try to write a html report I get the error,
>
>  >htmlReport(over_kegg, file = "KEGG.html")
> Error in function (classes, fdef, mtable)  :
>         unable to find an inherited method for function "htmlReport", 
> for signature "HyperGResult"
>
> any hints how to display the results ? (since Im quite lost by now)

I've added code to the devel version of the Category and GOstats
packages to support summary() and htmlReport() on the results of
hyperGTest when applied to KEGG, PFAM, and GO categories.

The updates will be availabe in the devel BioC repository tomorrow.
I'm considering patching the release with this code since it makes the
results much easier to display (I guess I can argue it is a bug of
omission).

I realized that I should have also pointed out how you can extract
some of the details from the result of a hyperGTest test with the
current versions.  Suppose you have created a parameter instance
'params' and done:

  ans <- hyperGTest(params)

Then you might try the following:

  pvalues(ans)[1:10]
  oddsRatios(ans)[1:10]
  expectedCounts(ans)[1:10]
  geneCounts(ans)[1:10]     ## Number of selected "genes" found in cateogry
  universeCounts(ans)[1:10] ## Number of "genes" in each tested category
  categoryIds <- names(pvalues(ans))

Best,

+ seth