[BioC] GOstat

[Seth Falcon]

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

> I am starting to use GOstat, and there are several things I do not
> understand.

Please let me know what parts are not clear.  I would like to improve
the documentation and make the code as easy to use as possible.

> I managed to get output from HyperGTest.  I was able to view the 
> enriched categories using htmlReport.
>
> I would like to try out the graphing methods, but I have not been 
> able to figure out the input.  In particular, I assume that since I 
> have created a GOHyperGResult object, I should use

The plot methods in GOstats are not very refined.  In part, this is
because it isn't always clear what picture one should draw.

So suggestions here would be welcome.

For example, given the result of a hyperGtest, one could plot all GO
terms significant at a specified p-value and show their relationships.
But that is a rather incomplete picture.  OTOH, if you expand the
graph by very much it becomes useless as you can't see anything once
you plot 100 nodes at once.

> getGoGraph
>
> but I have not figured out what goes into the goIds argument.  I 
> presume it is some type of node identifier, but where do I find it?

goIds should be a character vector of GO IDs, like "GO:xxxxxx".  

+ seth