run_all_metabolites_FBA2: Run full MIMOSA1 analysis on simulation data (2019)

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

Run full MIMOSA1 analysis on simulation data (2019)

Description

Run full MIMOSA1 analysis on simulation data (2019)

Usage

run_all_metabolites_FBA2(
  run_prefix,
  fake_spec,
  fake_mets,
  network,
  spec_codes,
  cor_method = "spearman",
  correction = "fdr",
  nperm = 10000,
  nonzero_filter = 4,
  kegg_translate = ""
)

Arguments

run_prefix
fake_spec	processed species table
fake_mets	processed metabolite table
network	output of build_metabolic_model
spec_codes	Table of species IDs
cor_method	spearman or pearson
correction	fdr or bonferroni
nperm	Number of Mantel permutations
nonzero_filter	Number of samples that must be nonzero for a metabolite to be included
kegg_translate	Compound ID table

Value

Output of run_all_metabolites

Examples

run_all_metabolites_FBA2("sim1", species, mets, network, spec_codes)

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