[BioC] Regarding KEGGgraph

[Wolfgang Huber]

Dear Anupam

the first thing you should try is upgrading to the most recent version 
of R and Bioconductor.

Next, if that does not help, please provide a reproducible example 
(others cannot see the files in your /home/anupam/ directory and hence 
not reproduce your problem, which almost always is a prerequisite for 
providing help).

	Best wishes
	Wolfgang

> Hi all,
>          I have downloaded the KGML files of for all the pathways of some
> organisms . I want to automate the process of constructing the metabolic
> networks of these organisms. In a directory by name ORG_XML_FILES I have the
> following directories and  files
> 
> /aac(dir)       /aae(dir)          etc ......
> 1.xml           4.xml
> 2.xml           5.xml
> 3.xml           6.xml
> 
> I want to enter each subdirectory (for e.g. aac) read all the xml files and
> construct a metabolic network using KEGGgraph
> 
> I have written the following script:
> 
> setwd("/home/anupam/Research/Anupam_data/ORG_XML_FILES/")
>  list.files()->org_xml_dirs
>  for (i in org_xml_dirs){
>  setwd(file.path("/home/anupam/Research/Anupam_data/ORG_XML_FILES/",i))
>  org_xml<-list.files()
>  for(j in org_xml)
>  {
>  graph_list<-pairlist()
>  graph<-parseKGML2Graph(j,genesOnly=TRUE)
>  graph_list<-c(graph_list,list(graph))
>  }
>  org_met_net<-mergeKEGGgraphs(graph_list)
>  met_org<-igraph.from.graphNEL(org_met_net,name=TRUE)
>  write.graph(met_org,"/home/anupam/Research/Anupam_data/ORG_XML_FILES/i.metnet",format=c("NCOL"))
>  }
> 
> But it is giving the following error :
> 
> Error in UseMethod("xmlAttrs", node) :
>   no applicable method for "xmlAttrs"
> 
> 
> here's my sessioninfo.
> 
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-redhat-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] KEGGgraph_1.1.0 graph_1.22.2    XML_2.5-1       igraph_0.5.2-2
> 
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
> 
> 
> Can anyone help me out with this ? thanks in advance.
> 
> Regards,
> 
> Anupam
> 
> 	[[alternative HTML version deleted]]
> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact