find_flux_variability_df {fbar}

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

Description

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

Usage

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

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.

Value

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