update_KEGG function

Update files from 'KEGG'

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

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.

Returns

No value