Question: problem with the structure of a list of pathways
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gravatar for Alberto Goldoni
10.4 years ago by
Alberto Goldoni60 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? 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
genetics pathways probe annaffy • 508 views
ADD COMMENTlink modified 10.4 years ago by James W. MacDonald51k • written 10.4 years ago by Alberto Goldoni60
Answer: problem with the structure of a list of pathways
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gravatar for James W. MacDonald
10.4 years ago by
United States
James W. MacDonald51k wrote:
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("

", x, "

", 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 10.4 years ago by James W. MacDonald51k
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