Given a metabolic model as a data frame, return a new data frame with fluxes and variability

This function calculates fluxes folds times with shuffled versions of the metabolic model. This is designed to detect and quantify underdetermined fluxes.

find_flux_variability_df(reaction_table, folds = 10, do_minimization = TRUE)

Arguments

reaction_table	a data frame representing the metabolic model
folds	number of times to calculate fluxes
do_minimization	toggle to uniformly minimize all non-objective fluxes after finding the objective

Value

reaction_table with two added columns: sd (the standard deviation of fluxes found) and flux (a typical flux) from this distribution

Details

This function uses ROI, so to solve models, you will need a solver plugin for ROI. Probably the easiest one to install is ROI.plugin.glpk. To install this in Linux, run sudo apt-get install libglpk-dev in a terminal, and then run install.packages('ROI.plugin.glpk') in R.