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Accio / KEGGgraph

The KEGGgraph package to parse KEGG pathways in R into graph objects
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Some KEGG nodes/ reactions are not retrieved #2

Closed Skourtis closed 4 years ago

Skourtis commented 4 years ago

Hi,

I'm trying to download the map00230 and retrieve the reactions from it. I'm using the following code.

tmp <- tempfile() retrieveKGML("map00230 ", organism="hsa", destfile=tmp, method="auto", quiet=TRUE) Metabo_Network <- KEGGpathway2reactionGraph(parseKGML(tmp))

nodes <- data.frame(id = str_remove_all(nodes(Metabo_Network),pattern= "cpd:"), stringsAsFactors = F)

but when I look for "C11821"/ "5-Hydroxyisourate" in the nodes data.frame its not there while it is present in the KEGG https://www.genome.jp/kegg-bin/show_pathway?map=map00230&show_description=show

Is there a reason for this? How could I solve it?

Thank you, Savvas

Skourtis commented 4 years ago

Sorry I realised that even though the compounds exist in the KEGG, the reactions doens't exist