generate_genomic_network: Create a community metabolic network model using a few...

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

Create a community metabolic network model using a few different methods.

Description

Create a community metabolic network model using a few different methods.

Usage

generate_genomic_network(
  kos,
  keggSource = "KeggTemplate",
  degree_filter = 0,
  minpath_file = "",
  normalize = T,
  rxn_table = "",
  networkFile = "",
  return_mats = T
)

Arguments

kos	Genes to include in network (KEGG Orthology IDs)
keggSource	source of network information, currently can be "KeggTemplate", "loadNet", or "metacyc"
degree_filter	Compounds connected to this number of KOs or more will be filtered from the network
minpath_file	file of minimal pathways to use for core network
normalize	Whether to normalize output matrix to show relative impacts of each gene on each compound
rxn_table	If keggSource is "KeggTemplate", must supply a data.table with the format of
networkFile	If keggSource is "loadNet", file that template network should be loaded from, should have same format as output of generate_network_template_kegg
return_mats	Whether to return stoichiometric matrices or just data.table list of reactions

Value

List containing 3 different versions of the same network: an adjacency matrix, an adjacency matrix that differentiates between genes with a neutral effect on a compound and no effect (0 vs NA), and an edge list.

Examples

generate_genomic_network(kos, "KeggTemplate", degree_filter = 30)

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