On 1/10/10 5:46 AM, anupam sinha wrote:
Hi Uwe,
Thanks for your suggestion . Here's my code. I am confused as
to how to initialize an empty list . Here I have used pairlist()
*list.files()->org_xml_dirs
## the following is much preferred:
org_xml_dirs <- list.files()
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_list <- list() ## in general, avoid 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"))
}
*
This is giving an error:
Error in UseMethod("xmlAttrs", node) :
no applicable method for "xmlAttrs"
I apologise for asking a Bioconductor list related question on this list.
Can you figure out the problem ? Thanks in advance.
Without output of sessionInfo() it is hard to diagnose further, but this
looks like a bug that has been resolved in latest version of the XML
package. Please make sure you are using the latest R release and latest
Bioconductor and CRAN packages.
+ seth
--
Seth Falcon
Bioconductor Core Team | FHCRC
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