Download KEGG pathways with related entrez ids

entrez_to_KEGG.R

library(KEGGREST)
library(org.Rn.eg.db)

# Download entrez ids and corresponding KEGG pathways followed
# by creation of a table where one column is entrez id and another 
# column is a comma separated list of KEGG pathways

# Download pathway to entrez id relationship
rno_path_eg  <- keggLink("pathway", "rno")
names(rno_path_eg) <- gsub("rno:", "", names(rno_path_eg))
rno_path_eg <- gsub("path:", "", rno_path_eg)
rno_path_eg <- data.frame(entrez_id = names(rno_path_eg),
                          kegg_id = rno_path_eg)
head(rno_path_eg)
dim(rno_path_eg)

# Create a table, where one column is an entrez id
# and the second column are comma separated pathways
# where this gene participates
rno_path_eg <- aggregate(kegg_id~entrez_id, rno_path_eg, paste, collapse=",")