get.pathways.by.genes: Client-side interface to obtain the KEGG pathway ids
In kozo2/keggapi: Client-side REST access KEGG

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/KEGGREST.R

Given a set of KEGG gene/enzyme/compound/reation identifiers, the functions query the KEGG PATHWAY database for all the pathways in which items represented by the given set of identifers are involved

 
get.pathways.by.genes(genes.id.list)
get.pathways.by.enzymes(enzyme.id.list)
get.pathways.by.compounds(compound.id.list)
get.pathways.by.reactions(reaction.id.list)

`genes.id.list`	`genes.id.list` a vector of character strings for the ids used by KEGG to represent genes. An id normally consists of three letters followed by a colon and then several numbers. The three letters are from the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern (e. g. hsa:111 for Homo Sapiens)
`enzyme.id.list`	`enzyme.id.list` a vector of character strings for enzyme commission numbers
`compound.id.list`	`compound.id.list` a vector of character strings for the ids used by KEGG to represent compounds. A compound id begins with cpd: followed by a combination of letters and numbers (e. g. cpd:C00579)
`reaction.id.list`	`reaction.id.list` a vector of character strings for the ids used by KEGG to represent reactions. A reaction id begins with rn: followed by a combination of letters and numbers (e. g. rn:R00268)

The functions return a vector of KEGG pathway ids

Kozo Nishida

http://www.kegg.jp/kegg/docs/keggapi.html

get.genes.by.pathway, get.enzymes.by.pathway, get.compounds.by.pathway, get.reactions.by.pathway

        # There seems to be some problem at the server side. Use try
        pathways <- try(get.pathways.by.genes(c("eco:b0077", "eco:b0078")))
        pathways <- try(get.pathways.by.enzymes("ec:1.3.99.1"))
        pathways <- try(get.pathways.by.compounds(c("cpd:C00033", "cpd:C00158"))) 
        pathways <- try(get.pathways.by.reactions(c("rn:R00959",
                                 "rn:R02740", "rn:R00960", "rn:R01786")))