[BioC] KEGGgraph problem

[Paul Shannon]

Hi Eric,

I see a couple of difficulties in your (nicely) provided code.  

Try this:

  dir(system.file("extdata",package="KEGGgraph"))

and you will see that hsa05200 is not amongh the 14 xml files included with the package.

Two suggestions:

1) If you wished to load one of those 14, you might have more success with this slight variation on what you wrote:

   filename <- system.file("extdata","hsa04010.xml",package="KEGGgraph")
   stopifnot(file.exists(filename))

Note that "extdata" needs to be included in the file path system.file helps you create.

2) To obtain files which are not included in the KEGGgraph package, take a look at

      ?retrieveKGML

I hope this helps.

 - Paul


On Jan 29, 2013, at 8:48 AM, eric [guest] wrote:

> 
> 
> Hi All,
> 
> I am running into a problem with KEGGgraph package. After loading
> all libraries and downloading hsa05200.xml I run:
> 
> cancerKGML <- system.file("hsa05200.xml",package="KEGGgraph");
> 
> but then, on running
> 
> cancerG <- parseKGML2Graph(cancerKGML,expandGenes=TRUE);
> 
> I get:
> Error: XML content does not seem to be XML, nor to identify a file name ''
> 
> Any ideas? Many thanks,
> Eric
> 
> 
> 
> 
> 
> -- output of sessionInfo(): 
> 
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=C                 LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] org.Hs.eg.db_2.7.1   KEGG.db_2.7.1        RSQLite_0.11.2      
> [4] DBI_0.2-5            AnnotationDbi_1.18.4 Biobase_2.16.0      
> [7] BiocGenerics_0.2.0   KEGGgraph_1.12.0     graph_1.34.0        
> [10] XML_3.95-0.1        
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.14.4 stats4_2.15.0  tools_2.15.0  
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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