get.pathways.by.genes {KEGGSOAP}R Documentation

Client-side interface to obtain the KEGG pathway ids

Description

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

Usage

 
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)

Arguments

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)

Value

The functions return a vector of KEGG pathway ids

Author(s)

Jianhua Zhang

References

http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

See Also

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

Examples

        # 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")))

[Package KEGGSOAP version 1.14.0 Index]