[BioC] pathway analysis package

Sean Davis sdavis2 at mail.nih.gov
Fri Dec 17 17:27:18 CET 2004

I haven't tried anything other than loading the XML file, but that is 
pretty straightforward.  Simply download the file:


Unzip it and change the first line to:

<?xml version="1.0" encoding="ISO-8859-1"?>

Then, in R, open the XML library:

biocarta <- xmlTreeParse(file='BioCarta.xml',asText=F)

Of course, BioCarta.xml has to be in the working directory or you must 
give the correct path.

You can then use the XML package to do manipulations of the resulting 


On Dec 17, 2004, at 9:29 AM, Saurin D. Jani wrote:

> Hi,
> Regarding Pathway analysis:
> In bioconductor when I load: library(KEGG)
> I can do this:
> kegg <- as.list(rae230aPATH2PROBE);
> and I can generate heatmap of pathway probes which are involved in my 
> DEgenes
> so, I can see which genes are up and down in perticular pathway.
> how can I use interaction data extracted from human BioCarta pathways 
> for my
> differentially expressed genes?
> if anyone has done please let me know...

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