build_species_networks_w_agora: Taxa mapping functions, MIMOSA2 June 2018 Finds close AGORA...

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

Taxa mapping functions, MIMOSA2 June 2018 Finds close AGORA models and then imports those for each species. Builds PICRUSt-based network for remaining species

Description

Taxa mapping functions, MIMOSA2 June 2018 Finds close AGORA models and then imports those for each species. Builds PICRUSt-based network for remaining species

Usage

build_species_networks_w_agora(
  mod_list,
  usePreprocessed = T,
  agora_path = "data/AGORA/",
  remove_sinks = T,
  add_rev = T
)

Arguments

usePreprocessed	Whether to process .mat files or use pre-computed versions
agora_path	Path to AGORA models
remove_sinks	Remove reactions that have NA as a substrate or product (usually uninformative transporters etc)
add_rev	Whether to add reverse of reversible reactions (default = T)
species_list	List of species from mapping

Value

A list with 2 entries - one a species abundance table in terms of the new species, the second a table of reactions for each species

Examples

build_species_networks_w_agora(species_table, "Greengenes 13_5 or 13_8", simThreshold = 0.99)

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