KEGG_pathway_ID2name.R

# function to retreive KEGG pathway names from KEGGREST. For some strange reasons, they won't take a list of queries even though the query size was set at 100. However, when I execute the query one path at a time, I would get an error message saying "Forbidden (HTTP 403)", hence the sys.sleep break. I am guess querying more than 100 within a short period of time would not be allowed too. I'm expecting a KEGGgraph input of graphs with path ID that are like "X00010", but feel free to remove the gsub function if you have already formatted your pathID into the "map00010" form.

library(KEGGREST)

kegg_all_names <- function(pathID) {
  repeats <- floor(length(pathID) / 100)
  final_rep <- length(pathID) %% 100
  pathNames <- NULL
  for (i in 1:repeats) {
    pathNames <- c(pathNames, unlist(lapply(gsub("X", "map", pathID[(1 + (i * 100) - 100):(i * 100)]), function(x) keggFind("pathway", x))))
    Sys.sleep(5)
  }
  pathNames <- c(pathNames, unlist(lapply(gsub("X", "map", pathID[(1 + (i * 100)):(i * 100 + final_rep)]), function(x) keggFind("pathway", x))))
  return(pathNames)
}