Hi dear Robert,

   Thanks for reporting! Would you please send the file you used? I will try
to figure out what went wrong.

  Best wishes,
David

2010/7/7 Robert M. Flight <rflight79@gmail.com>

> 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:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] KEGGgraph_1.4.0  Rgraphviz_1.26.0 graph_1.26.0     XML_3.1-0
>
> loaded via a namespace (and not attached):
> [1] 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@louisville.edu
> EM rflight79@gmail.com
>
> Williams and Holland's Law:
>       If enough data is collected, anything may be proven by
> statistical methods.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Jitao David Zhang
Pre-doc staff of Computational Biology and Biostatistics
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

	[[alternative HTML version deleted]]

