find_flux_variability_df: Given a metabolic model as a data frame, return a new data...
In fbar: An Extensible Approach to Flux Balance Analysis

Description Usage Arguments Details Value

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

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

`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

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.

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

fbar documentation built on Sept. 2, 2020, 5:08 p.m.