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Kegg Graph not proper xml

I am new to KEGG graph. I am trying to parse the KGML to get a graph but I get an error saying the KEGG xml is not xml format. Here is my code and error :

library(KEGGgraph)
tcell<- system.file( "extdata/hsa04350.xml", package="KEGGgraph")
map.t<-parseKGML2Graph(tcell)
plot(map.t)

And the error i get on step 3 is: 

Error: XML content does not seem to be XML: ''

How can I handle this ?

rna-seq kegg
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written by saamar.rajput saamar.rajput

1 answer

what's the output of

file extdata/hsa04350.xml

if it's not something like:

extdata/hsa04350.xml: XML  document text

then...

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I am sorry I did not understand your question. Did you mean output of tcell ?

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written by saamar.rajput saamar.rajput

Thank you so much Pierre, I think I figured out what went wrong :)

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written by saamar.rajput saamar.rajput

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