Download all pathways — retrieve_all

Download all KEGG pathways for a given organism

Usage

retrieve_all_pathways(org, wait = 0.5, verbose = FALSE)

Arguments

org: KEGG organism code (e.g., 'hsa' for human).
wait: Numeric value, needs to be strictly positive. Indicates the amount in seconds to wait in between requests, being polite and respectful of the limit rates imposed by KEGG. Defaults to 0.5, which is safely a bit above the rate of 3max/sec.
verbose: Logical, if TRUE, print additional messages.

Value

The BiocFileCache object is returned invisibly

Details

This function can take a while to run completely, but is an efficient way to retrieve all the kgml files encoding for the KEGG pathways. Some failures could be triggered by a rate limitation imposed by the KEGG website. Since this caches the files locally, it is safe to rerun to complete the operation without extra unneeded requests to the API

Examples

# Download all pathways for human
if (FALSE) { # \dontrun{
  retrieve_all_pathways("hsa", verbose = TRUE)
} # }