get.pathways.by.genes {KEGGSOAP} | R Documentation |
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
Jianhua Zhang
http://www.genome.jp/kegg/soap/doc/keggapi_manual.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")))