Hi Seth, Thanks I found one way around my problem (for the non devel version of the package Category): geneIds(hgOver)[geneIds(hgOver) %in% hgOver at catToGeneId[[i]]] where [[i]] runs over significant KEGG terms obtained from hyperGTest(params). Cheers, Ivan Quoting Seth Falcon <sfalcon at="" fhcrc.org="">: > Hi Ivan, > > ivan.borozan at utoronto.ca writes: >> I've used the script below to calculate over-represented KEGG >> categories however I can not get to gene ID's associated with each of >> the overrepresented KEGG terms/pathways ? > > I've been working on making results easier to work with and also > improving the documentation. This is all happening in the devel arm > (which will soon become the next release). > > With a (very) recent version of Category you can get help on all > accessors for the result objects returned by hyperGTest: > > help("HyperGResult-accessors") > >> My question, does catToGeneId() exist and how do I get to genes that >> are associated with each of the above pathways ? > > To get the category to universe of gene IDs mapping: > > > geneIdUniverse(ans)[1:2] > $`00625` > [1] "YCR105W" "YCR107W" "YDL243C" "YDR368W" "YFL056C" "YHR104W" > "YJR155W" > [8] "YKR009C" "YNL331C" "YOR120W" > > $`04010` > [1] "YAL041W" "YBL016W" "YBL105C" "YBR083W" "YBR200W" "YCL027W" > "YDL159W" > [8] "YDL235C" "YDR103W" "YDR461W" "YDR480W" "YER111C" "YER118C" > "YFL026W" > [15] "YGL089C" "YGR032W" "YGR040W" "YGR088W" "YHL007C" "YHR005C" > "YHR030C" > [22] "YHR084W" "YIL147C" "YJL095W" "YJL128C" "YJL157C" "YJR086W" > "YKL062W" > [29] "YKL178C" "YKR095W" "YLR006C" "YLR113W" "YLR182W" "YLR229C" > "YLR332W" > [36] "YLR342W" "YLR362W" "YML004C" "YMR037C" "YMR043W" "YNL053W" > "YNL098C" > [43] "YNL145W" "YNL271C" "YNL283C" "YNR031C" "YOL105C" "YOR008C" > "YOR212W" > [50] "YOR231W" "YPL049C" "YPL089C" "YPL140C" "YPL187W" "YPR165W" > > To get the category to _selected_ gene IDs mapping: > > > geneIdsByCategory(ans)[1:2] > $`00625` > [1] "YOR120W" > > $`04010` > [1] "YFL026W" "YLR342W" > > The number of selected genes in each category (just the length of each > element of the above): > > > geneCounts(ans)[1:2] > 00625 04010 > 1 2 > > NOTE: I used the YEAST annotation data package as an example. It is > non-typical in that it does not use Entrez Gene IDs as the base > identifier. For your example, you will get Entrez IDs and you can map > those to SYMBOL if you want using the appropriate annotation data > package. > > The above examples were done using: > > R 2.5.0 beta, Category 2.1.36 > > sessionInfo() > R version 2.5.0 beta (--) > powerpc-apple-darwin8.9.0 > > locale: > C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" > [7] "utils" "methods" "base" > > other attached packages: > YEAST Category AnnotationDbi RSQLite DBI > "1.15.13" "2.1.36" "0.0.58" "0.5-4" "0.2-1" > Matrix lattice genefilter survival annotate > "0.9975-11" "0.15-3" "1.13.12" "2.31" "1.13.7" > GO KEGG graph Biobase > "1.15.13" "1.15.13" "1.13.10" "1.13.48" > > Hope that helps. > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center > http://bioconductor.org >