View source: R/core_functions.R
generate_network_template_kegg | R Documentation |
Generate community metabolic network template from the KEGG database, using reaction_mapformula.lst
generate_network_template_kegg(
mapformula_file,
all_kegg,
write_out = T,
remove_extra_pathways = T
)
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 |
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)
generate_network_template_kegg("KEGG/ligand/reaction/reaction_mapformula.lst", all_kegg)
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