run_shuffle: Run one iteration of MIMOSA analysis with a randomized...

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

Run one iteration of MIMOSA analysis with a randomized metabolic network. Run this function many times to generate a null distribution of metabolite comparisons.

Description

Run one iteration of MIMOSA analysis with a randomized metabolic network. Run this function many times to generate a null distribution of metabolite comparisons.

Usage

run_shuffle(
  out_file,
  id_num = 1,
  n_iter = 5000,
  nonzero_filter = 3,
  qval_thresholds = c(0.1, 0.01)
)

Arguments

out_file	File path to .Rda file of MIMOSA output from run_all_metabolites
id_num	ID number of shuffle (if running many iterations)
n_iter	Number of edge switches to generate randomized network, default is 5000
nonzero_filter	Minimum number of samples required to have nonzero concentrations and nonzero metabolic potential scores in order for metabolite to be evaluated, default is 3
qval_thresholds	1 or more significance thresholds above which to count the number of metabolites

Value

None, writes two tables to file - one of the total counts of metabolites meeting each threshold, and one of the results for each metabolite

Examples

run_shuffle("Dataset2_bv_out.rda", id_num = 1)

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