[BioC] problem with the structure of a list of pathways

[James MacDonald]

Hi Alberto,

I answered the first version of this question (I see my email in my sent 
folder), but evidently it didn't make it past that point. I have 
re-created this answer below.

HOWEVER, this is the third (third!) time you have asked this question in 
slightly different ways on this list. I give you an A for perseverance, 
but a D- for getting the hint that maybe nobody is going to answer your 
question and trying to figure it out yourself.


-- 

James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826


>>> Alberto Goldoni <alberto.goldoni at segesta.pro> wrote:
> Dear all,
> 
> i have a problem with the package annaffy. As the vignette says i can save 
> an HTML page (example1.html):
> 
> anncols <- aaf.handler()[c(1:3, 8:9, 11:13)]
> anntable <- aafTableAnn(probeids[1:50], "hgu95av2.db", anncols)
> saveHTML(anntable, "example1.html", title = "Example Table without Data")
> 
> the HTML page present a list of probes and for each probe you can found many 
> informations like:
> 
> 1] "Probe" "Symbol" "Description"
> [4] "Chromosome" "Chromosome Location" "GenBank"
> [7] "Gene" "Cytoband" "UniGene"
> [10] "PubMed" "Gene Ontology" "Pathway"
> 
> 
> Now it is possible to have a list of pathways and for each pathway to have 
> the probes that have the same pathway?

Now to the answer...

The answer, as with most questions about R is 'Yes, of course.".
However, not using annaffy, which is designed to do one particular type
of table. You don't say if you need links or not, but if you just want
an HTML table mapping pathways to genes (where by gene you really appear
to mean reporter or probeset ID).

## fake up some data

  > library(hgu95av2.db)
  > lst <- mget(Lkeys(hgu95av2PATH)[1:10], hgu95av2PATH)

## little function to make life easier

  > getRows <- function(x) {
          paste("<P>", x, "</P>", collapse = "", sep = "")
      }

  > tmp <- data.frame(names(lst), sapply(lst, getRows))
  > print(xtable(tmp), type="html", file="tmp.html",
include.rownames=FALSE, sanitize.text.function=function(x) x)

Best,

Jim

> 
> 
> Best regards.
> 
> -----------------------------------------------------
> Alberto Goldoni, PhD
> IT Lan Manager
> Medical Genetics Unit
> S. Orsola-Malpighi Hospital
> Via Massarenti n.9, Pad 11
> 40100 Bologna, Italy
> Fax: 051-636-4004
> alberto.goldoni at eurogene.org 
> www.eurogene.org 
> www.lagem.it 
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