Get KEGG db with caching.

Get KEGG db with caching.

Usage

get_kegg_db(
  db_name = "compound",
  directory = NULL,
  bfc = NULL,
  verbose = FALSE
)

Arguments

db_name

Name of the KEGG database to retrieve (default: "compound").

directory

Optional directory to save the KEGG database file if not using cache.

bfc

BiocFileCache object for caching KEGG database files.

verbose

Logical, if TRUE, print additional messages.

Value

A data frame with KEGG IDs and names.

Details

The valid KEGG database names are: kegg | pathway | brite | module | ko | genes | | vg | vp | ag | genome | ligand | compound | glycan | reaction | rclass | enzyme | network | variant | disease | drug | dgroup

Examples

# Saving in directory
data_dir <- tempdir()
kegg_compounds <- get_kegg_db("compound", directory = data_dir, verbose = TRUE)
#> Retrieving KEGG database: compound
#> Downloaded & saved KEGG database in: /tmp/Rtmpf7h8iD/kegg_compound.tsv
# Just returning without saving
kegg_genes <- get_kegg_db("compound", verbose = TRUE)
#> Retrieving KEGG database: compound
#> No 'bfc' or 'directory' provided. Not saving KEGG database only downloading and returning.