update_KEGG {ReporterScore}

Update files from 'KEGG'

Description

Download links:

https://rest.kegg.jp/list/pathway https://rest.kegg.jp/link/pathway/ko https://rest.kegg.jp/link/pathway/compound https://rest.kegg.jp/list/module https://rest.kegg.jp/link/module/ko https://rest.kegg.jp/link/module/compound

Usage

update_KEGG(download_dir)

update_KO_file(download_dir, RDSfile = NULL)

update_htable(type, keg_file = NULL, download = FALSE, download_dir = NULL)

update_org_pathway(
  org = "hsa",
  RDS_file = NULL,
  download = TRUE,
  download_dir = NULL
)

Arguments

download_dir

where to save the .keg file?

RDSfile

saved KO_files.RDS file

type

"ko", "module", "pathway", "compound" ...

keg_file

path of a .keg file, such as ko00001.keg from https://www.genome.jp/kegg-bin/download_htext?htext=ko00001&format=htext.

download

save the .keg file?

org

kegg organism, listed in https://www.genome.jp/kegg/catalog/org_list.html, default, "hsa"

RDS_file

path of a org.RDS file if you saved before.

Value

No value