update_KEGG: Update files from 'KEGG'

In ReporterScore: Generalized Reporter Score-Based Enrichment Analysis for Omics Data

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

ReporterScore documentation built on Sept. 11, 2024, 6:44 p.m.