Good day all,
I have a question which I can't seem to find a specific answer for - is it possible to query KEGG via keggrest in R, and return organism specific pathways for kegg compound ids?
For example in Arabidopsis -
for genes - I can do this - linkd_data<-keggLink("pathway","ath:AT1G22430")
and get
> linkd_data[[1]]
[1] "path:ath00010"
where this is arabidopsis specific pathway (or general pathways which are known to be in arabidopsis) as explained here - https://www.genome.jp/kegg/kegg3a.html
or I can do this as well - pathways.list <- keggList("pathway", "ath")
to get the entire flatfile for ATH specific pathways.
So I was trying to do this for compounds - comp_data<-keggLink("pathway","cpd:C00001")
For which I get back -
comp_data[[1]]
[1] "path:map00190"
the pathways returned being the reference pathways as explained in the link above.
Is there any variation of kegglink() or another function/command to specifically get arabidopsis (or any other organism) specific pathways given certain compound KEGG ids?
any help would be appreciated. Thanks!
I am not sure, as I have never used KEGGREST. Do the examples here help? - https://www.bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html