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

Source: R/convenience_wrappers.R

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

find_fluxes_df(reaction_table, do_minimization = FALSE)

Arguments

reaction_table

a data frame representing the metabolic model
do_minimization

toggle to uniformly minimize all non-objective fluxes after finding the objective

Value

The input data frame with a new numeric column, "flux".

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.

See also

find_fluxes_vector

Examples

if (FALSE) {
data(ecoli_core)
ecoli_core_with_flux <- find_fluxes_df(ecoli_core)
}