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Robert M. Flight ▴ 280@robert-m-flight-4158
Last seen 6 weeks ago
Hi All, I'm playing around with KEGGGraph to examine some pathways, and I am running into some errors. When I try to plot some pathways, I get the error: "Error in .subtypeDisplay(object) : Given subtype 'missing interaction' is not found!" Here is an example with one pathway that gives the error and another that does not: library(KEGGgraph) # this one gives the error keggID <- "05213" tmpXML <- "testKGML1.xml" retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget") tmpGraph1 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) plotKEGGgraph(tmpGraph1) # this one does not give an error, and spits out a very complicated graph keggID <- "04810" tmpXML <- "testKGML2.xml" retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget") tmpGraph2 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) plotKEGGgraph(tmpGraph2) Any help on why this error is cropping up would be appreciated. R version 2.11.1 (2010-05-31) 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:  grid stats graphics grDevices utils datasets methods  base other attached packages:  KEGGgraph_1.4.0 Rgraphviz_1.26.0 graph_1.26.0 XML_3.1-0 loaded via a namespace (and not attached):  tools_2.11.1 Thanks in advance, -Robert Robert M. Flight, Ph.D. Bioinformatics and Biomedical Computing Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.flight at louisville.edu EM rflight79 at gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods.