run_mimosa1: Run full MIMOSA1 analysis (2019)

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

Run full MIMOSA1 analysis (2019)

Description

Run full MIMOSA1 analysis (2019)

Usage

run_mimosa1(
  species,
  mets,
  species_file = "mimosa1",
  picrust_file_paths = c("data/picrustGenomeData/16S_13_5_precalculated.tab.gz",
    "data/picrustGenomeData/indivGenomes/", "_genomic_content.tab"),
  rxn_path = "data/KEGG/full_rxn_table.txt",
  simulated = F,
  config_table = NULL
)

Arguments

species	processed species table
mets	processed metabolite table
species_file	File prefix from species data or other ID for saving
picrust_file_paths	paths to picrust1 files
rxn_path	Path to processed mapformula reaction table
simulated	Whether this is simulated data
config_table	A MIMOSA2 configuration table of analysis settings (required only for using simulation data)

Value

Output of run_all_metabolites

Examples

run_mimosa1(species, mets)

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