Maybe not directly, but note that htmlReport() is simply using xtable
create the HTML page using the output from summary(). So you could
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,
Note that the categorySize argument isn't necessary, but does protect
you from choosing arguably spurious results (like a GO term with 3
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
to separate each ID with a
, so you will need to
either cat() or paste() things together. Once you have that, just add
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
a bit of work, and could get really messy if there are dozens of
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:
> is there any way to get additional information into the hyperGTest
> Specifically, I would like to include the Entrez IDs for the genes
> contributing to
> each overrepresented GO term.
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives:
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109