[BioC] problem with GOHyperGParams in package Category

[Seth Falcon]

On Thu, Mar 6, 2008 at 7:32 AM, Tony Chiang <tchiang at fhcrc.org> wrote:
> As far as I know, GOstats depends on Category, so that the user can
> create the GOHyperGParams class and then use the other functions and
> methods in GOstats to carry out the rest of the analysis. In the
> past, there has been some hiccups when there is bilateral
> dependencies, but maybe this has been resolved.

Yes, GOstats depends on Category (one way to verify is by inspecting
the DESCRIPTION files).

Circular dependencies (the Depends field) don't work.  I believe it is
possible to have cycles in the Suggests field.  Whether or not having
Category suggest GOstats would improve matters I'm less certain.

>  I can see your point in that you can perform the categorical
>  analysis for KEGG or pFAM using Category alone, but need to load
>  GOstats for the GO analysis. It is a minor confusing issue I agree,
>  but I am sure that Robert and Seth had a good reason to structure
>  the packages as they are.

It is more confusing than I would like, but there was some thought
given to the current organization.  At the time it made sense to
remove the common code for Hypergeometric testing from GOstats since
there is nothing GO-specific about that code.  Category seemed the
most natural landing place and was already a dependency of GOstats.

The intention was to be able to perform GO analyses just using
Category.  GOstats adds the ability to perform the conditional
analysis.

Anyhow, I share your frustration at the organization.  I think the end
result is somewhat more difficult for end users than I would like.
However, I don't have a better solution at present.

+ seth

--
Seth Falcon | seth at userprimary.net | http://userprimary.net/user/