[BioC] hyperGTest

Seth Falcon sfalcon at fhcrc.org
Tue May 1 00:13:38 CEST 2007

Naomi Altman <naomi at stat.psu.edu> writes:

> I am having some problems with hyperGTest.  See below.  Also, I 
> wanted to modify hyperGTest for my project, but I cannot seem to find 
> any relevant code.  There must be some secret to names for functions 
> for this type of thing - please point me in the right direction.

As Jim pointed out, you need the Matrix package.  This should have
come along with an install of GOstats via biocLite(), but perhaps you
installed using another mechanism.

As for modifying the code for your project, you will want to download
and unpack the source packages (.tar.gz) for Category and GOstats.
The code is split between these packages since much of the
Hypergeometric testing is not GO specific.

There are a few notes in the man page for hyperGTest for how to extend
to other category types if that is what you want to do.

Given that you didn't have GOstats properly loaded, I imagine all of
its functions would be rather invisible ;-)


+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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