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Get a KEGG database file

Source: R/api_interfaces.R
get_kegg_db.Rd

Get KEGG database, with caching.

Usage

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

Arguments

db_name

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

path

Optional path to save the KEGG database file if not using cache. Defaults to NULL.

bfc

BiocFileCache object for caching KEGG database files. Defaults to NULL

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 path
data_dir <- tempdir()
kegg_compounds <- get_kegg_db(
  db_name = "compound",
  path = data_dir, verbose = TRUE
)
#> Retrieving KEGG database: compound
#> Downloaded & saved KEGG database in: /tmp/RtmpkwIYXN/kegg_compound.tsv

# Just returning without saving
kegg_compounds_onthefly <- get_kegg_db(
  db_name = "compound",
  verbose = TRUE
)
#> Retrieving KEGG database: compound
#> No 'bfc' or 'path' provided.
head(kegg_compounds_onthefly)
#>   kegg_id
#> 1  C00001
#> 2  C00002
#> 3  C00003
#> 4  C00004
#> 5  C00005
#> 6  C00006
#>                                                                                                                                                  description
#> 1                                                                                                                                                 H2O; Water
#> 2                                                                                                                             ATP; Adenosine 5'-triphosphate
#> 3                                                         NAD+; NAD; Nicotinamide adenine dinucleotide; DPN; Diphosphopyridine nucleotide; Nadide; beta-NAD+
#> 4                                                                                                      NADH; DPNH; Reduced nicotinamide adenine dinucleotide
#> 5                                                                                           NADPH; TPNH; Reduced nicotinamide adenine dinucleotide phosphate
#> 6 NADP+; NADP; Nicotinamide adenine dinucleotide phosphate; beta-Nicotinamide adenine dinucleotide phosphate; TPN; Triphosphopyridine nucleotide; beta-NADP+

# saving to cache (in a temp dir)
kegg_compounds_cached <- get_kegg_db(
  db_name = "compound",
  bfc = BiocFileCache::BiocFileCache(tempdir()),
  verbose = TRUE
)
#> Retrieving KEGG database: compound
#> adding rname 'https://rest.kegg.jp/list/compound'
#> 
#> Cached KEGG database: compound