generate_network_template_kegg: Generate community metabolic network template from the KEGG...

View source: R/core_functions.R

generate_network_template_keggR Documentation

Generate community metabolic network template from the KEGG database, using reaction_mapformula.lst

Description

Generate community metabolic network template from the KEGG database, using reaction_mapformula.lst

Usage

generate_network_template_kegg(
  mapformula_file,
  all_kegg,
  write_out = T,
  remove_extra_pathways = T
)

Arguments

mapformula_file

file path to "reaction_mapformula.lst" from the KEGG database, specifying reaction IDs annotated in pathways

all_kegg

Output of get_kegg_reaction_info, OR vector of 2 file paths to input to get_kegg_reaction_info

write_out

Whether to save template to file

Value

A table specifying a community metabolic network based on KEGG pathways with the following columns: Rxn (reaction ID), KO (Gene ID), Reac (Reactant ID), Prod (Product ID), Path (Pathway ID), ReacProd (Original reaction specification), stoichReac (Reactant stoichiometry coefficient), stoichProd (Product stoichiometry coefficient)

Examples

generate_network_template_kegg("KEGG/ligand/reaction/reaction_mapformula.lst", all_kegg)

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