[BioC] GOstat

[James W. MacDonald]

Hi Naomi,

Naomi Altman wrote:
> I am starting to use GOstat, and there are several things I do not understand.
> 
> 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
> 
> 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?

The getGoGraph() function wants a GOHyperGParams object, rather than a 
GOHyperGResult object. The goIds would then be the GO IDs that you are 
interested in, which can be read from the table produced by htmlReport().

Anyway, I can't get getGoGraph() to ouput what I would expect. It 
appears to use GOXXCHILDREN to produce the graph, whereas the other 
functions in the examples for that (and related) function(s) use 
GOXXPARENTS.

To get what I would expect, you can simply use GOGraph(). Say the top 
three GO IDs in your table are ("GO:0019219" "GO:0019222" "GO:0006350"). 
Then you can get a graph by:

grph <- GOGraph(c("GO:0019219" "GO:0019222" "GO:0006350"), GOBPPARENTS)
plot(grph)

HTH,

Jim


> 
> Thanks for any assistance.
> 
> Naomi
> 
> 
> 
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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