Hi Seth,

On Thu, Mar 6, 2008 at 9:48 PM, Seth Falcon <seth@userprimary.net> wrote:

> On Thu, Mar 6, 2008 at 7:32 AM, Tony Chiang <tchiang@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.
>

I think that Mark's question about adding an Error Statement would be a good
compromise solution, no? There have been more than a few people who just
expect the conditional GO analysis to work when they simply load Category.
Knowing this, if they can't access the class or methods defined in GOstats,
an error message stating that they should try to load GOstats might be a
simple work around.

It also might be worthwhile to put this in the documentation for  the
GOHyperGParams class. As the man page stands right now, there is
documentation for the "conditional" logical parameter (for which there
should be), but no explicit statement that all of the functionality when
conditional = TRUE only works if GOstats is loaded as well and that GOstats
is not automatically loaded. If I were a newbie and looked at the
documentation, I would assume that the conditional testing should work
within the scope of the Category package (and its dependencies).

>
> + seth
>
> --
> Seth Falcon | seth@userprimary.net | http://userprimary.net/user/
>

tc

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