[BioC] GOstat

[James W. MacDonald]

Hi Seth,

Seth Falcon wrote:
> 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".

Consider the following code:

library(hgu133plus2)
library(GOstats)
library(Rgraphviz)
lls <- unlist(as.list(hgu133plus2ENTREZID))[1:500]
lls <- lls[!is.na(lls)]
univ <- unlist(as.list(hgu133plus2ENTREZID))
univ <- univ[!is.na(univ)]
params <- new("GOHyperGParams", geneIds=lls, universeGeneIds=univ, 
ontology="BP", annotation="hgu133plus2", conditional=TRUE)
hypt <- hyperGTest(params)
grph1 <- getGoGraph(params, summary(hypt)[1:3,1])
plot(grph1)
grph2 <- GOGraph(summary(hypt)[1:3,1], GOBPPARENTS)
plot(grph2)

Is the intent that the two graphs should be identical? My reading of the 
help page leads me to believe so.

Best,

Jim

> 
> + seth
> 
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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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