get_kegg_reaction_info: Get basic KEGG reaction and KO info in a unified format

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Get basic KEGG reaction and KO info in a unified format

Description

Get basic KEGG reaction and KO info in a unified format

Usage

get_kegg_reaction_info(
  kos_to_rxns_method,
  reaction_info_file = "",
  save_out = T,
  kolist = ""
)

Arguments

kos_to_rxns_method	EITHER "KEGGREST" indicating to use the KEGGREST API to link KOs and reactions and get reaction info, OR a file path to the KEGG file genes/ko/ko_reaction.list
reaction_info_file	If kos_to_rxns_method is a file path, additional file containing full reaction info from the KEGG database
save_out	whether to save output as an Rdata file named "KeggReactions.rda"
kolist	Optionally, a vector of KO IDs. Will create an all_kegg object containing information only on those KOs and the reactions linked to them.

Value

An R object with 4 components: a list of KOs, a list of Reaction IDs, a list of associated reaction info, and a table linking KOs to reactions

Examples

get_kegg_reaction_info("KEGGREST")
get_kegg_reaction_info("KEGG/genes/ko/ko_reaction.list", "KEGG/ligand/reaction/reaction")

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.