KEGGgraph question
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Sim, Fraser ▴ 350
@sim-fraser-2871
Last seen 8.1 years ago
Hi David, I have been using the KEGGgraph package to plot Kegg pathways. I am working on the glioma pathway "05214". The compounds that are present in this library are not displaying their names as indicated from the KEGG website for example: Here is the result of a "getKEGGnodeData" on node cpd:C00076. KEGG Node (Entry 'cpd:C00076'): ------------------------------------------------------------ [ displayName ]: C00076 [ Name ]: cpd:C00076 [ Type ]: compound [ Link ]: http://www.genome.jp/dbget-bin/www_bget?compound+C00076 ------------------------------------------------------------ The link shows the name Calcium;Ca2+ on the website. Is there any way of retrieving this from the Kegg XML using your package? Thanks, Fraser [[alternative HTML version deleted]]
Pathways KEGGgraph Pathways KEGGgraph • 684 views
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Entering edit mode
Sim, Fraser ▴ 350
@sim-fraser-2871
Last seen 8.1 years ago
Hi David, Here's the result: > library(KEGGgraph) > library(Rgraphviz) > KeggID = "04310" > KEGGpathway = parseKGML(getKGMLurl(KeggID, organism = "hsa")) > keggG = KEGGpathway2Graph(KEGGpathway, genesOnly = FALSE, expandGenes = TRUE) > getDisplayName(keggGnodedata[["cpd:C00076"]]) [1] "C00076" I think it should be Calcium;Ca2+ Cheers, Fraser > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rgraphviz_1.21.7 RBGL_1.18.0 KEGGgraph_0.8.15 graph_1.20.0 [5] XML_1.99-0 rcom_2.0-4 rscproxy_1.0-12 loaded via a namespace (and not attached): [1] cluster_1.11.12 tools_2.8.1 From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: Monday, March 16, 2009 2:23 AM To: Sim, Fraser Subject: Re: KEGGgraph question Hi Fraser, ? Sorry for the late reply, have you tried getDisplayName? Best wishes, David 2009/3/3 Sim, Fraser <fraser_sim at="" urmc.rochester.edu=""> Hi David, ? I have been using the KEGGgraph package to plot Kegg pathways. I am working on the glioma pathway "05214". The compounds that are present in this library are not displaying their names as indicated from the KEGG website for example: ? Here is the result of a "getKEGGnodeData" on node cpd:C00076. ? KEGG Node (Entry 'cpd:C00076'): ------------------------------------------------------------ [ displayName ]: C00076 [ Name ]: cpd:C00076 [ Type ]: compound [ Link ]: http://www.genome.jp/dbget-bin/www_bget?compound+C00076 ------------------------------------------------------------ ? The link shows the name Calcium;Ca2+ on the website. Is there any way of retrieving this from the Kegg XML using your package? ? Thanks, Fraser -- Cheers, David
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