Hello,
I'm trying to retrieve KEGG pathway names after Enrichment Analysis using KEGG.db from Bioconductor.
library(KEGG.db)
# a key value pair: pathways to entrez id
pathway2entrez <- as.list(KEGGPATHID2EXTID)
head(pathway2entrez)
Now let's say I found the pathway hsa00232 significantly enriched. I would like to get a name for this pathway. But I didn't find a map in the variables of KEGG* from the pathway ID (in the form hsa*) to pathway name. Can someone give me a hint how I can do this?
2 answers
I don't know how/if this is implemented in KEGG.db or other Bioconductor packages, but retrieval of pathway name from ID is easy using the TogoWS REST service. The URL for your example is:
http://togows.dbcls.jp/entry/pathway/hsa00232/name
In R you could use e.g. RCurl:
library(RCurl)
getURL("http://togows.dbcls.jp/entry/pathway/hsa00232/name")
# [1] "Caffeine metabolism - Homo sapiens (human)\n"
There is this object: KEGGPATHID2NAME in KEGG.db, which does what you want, but it takes KEGG id in number form only, so you have to remove the leading "hsa" first:
> library(KEGG.db)
> keggid <- "hsa00232"
> keggid2keggname <- as.list(KEGGPATHID2NAME)
> keggid2keggname[substring(keggid, 4)]
$`00232`
[1] "Caffeine metabolism"
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