[BioC] hyperGTest html report

James W. MacDonald jmacdon at med.umich.edu
Wed Jan 9 16:50:39 CET 2008

Hi Sebastien,

Maybe not directly, but note that htmlReport() is simply using xtable to 
create the HTML page using the output from summary(). So you could just 
create the table and then add a column of Entrez Gene IDs and then 
output the result.

Say your GOHyperGResult object is called 'hypt':

out <- summary(hyp, summary.args=list(htmlLinks=TRUE, categorySize=10))

Note that the categorySize argument isn't necessary, but does protect 
you from choosing arguably spurious results (like a GO term with 3 genes 
in the universe and 1 that was significant).

Now you are going to have to create a vector containing all the Entrez 
Gene IDs for each GO term. For this to work in HTML, you will also need 
to separate each ID with a <P>EntreGeneID</P>, so you will need to 
either cat() or paste() things together. Once you have that, just add to 
the data.frame created above:

out <- data.frame(out, entregeneidvector)
xtab <- xtable(out, caption="A Caption", digits=rep(c(3,0), c(4,8)))
print(xtab, type="html", file="A file name.html", 
caption.placement="top", sanitize.text.function=function(x) x, 

HOWEVER, that might not really be what you want, as it will obviously be 
a bit of work, and could get really messy if there are dozens of Entrez 
Gene IDs for a particular GO term. An alternative is to output 
individual HTML tables for each GO term of interest that list out the 
probesets that contributed to the significance of that term. For that 
you might want to look at hyperGoutput() in the affycoretools package.



Sebastien Gerega wrote:
> Hi,
> is there any way to get additional information into the hyperGTest html 
> report?
> Specifically, I would like to include the Entrez IDs for the genes 
> contributing to
> each overrepresented GO term.
> thanks,
> Sebastien
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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