add_to_network: Add reactions to a network. Will set stoichiometry and copy...

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

Add reactions to a network. Will set stoichiometry and copy number to 1 if missing. Format can be either "KO, Rxn, Prod" for reaction IDs with all transformations and correct stoichiometry, or just "KO" but with reaction IDs that are defined in the KEGG network.

Description

Add reactions to a network. Will set stoichiometry and copy number to 1 if missing. Format can be either "KO, Rxn, Prod" for reaction IDs with all transformations and correct stoichiometry, or just "KO" but with reaction IDs that are defined in the KEGG network.

Usage

add_to_network(
  network,
  addTable,
  target_format = NULL,
  source_format = NULL,
  kegg_path = "data/KEGG/",
  data_path = "data/"
)

Arguments

network	Data.table of taxa, genes and reactions
addTable	Data.table of taxa, genes and/or reactions to add, or generic genes and reactions to be applied to all taxa
target_format	Format of taxa, genes, and/or reactions to add - must be "KEGG" or "Cobra". If NULL, will try to guess
source_format	Format of taxa, genes, and/or reactions to add - must be "KEGG" or "Cobra". If NULL, will try to guess
kegg_path	Path to KEGG database
data_path	Path to reference data with AGORA-KEGG mappings

Value

Expanded network table

Examples

add_to_network(network, netAddTable)

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