find_fluxes_df: Given a metabolic model as a data frame, return a new data...

In maxconway/fbar: An Extensible Approach to Flux Balance Analysis

Description

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

Usage

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

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

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

See Also

find_fluxes_vector

Examples

## Not run: 
data(ecoli_core)
ecoli_core_with_flux <- find_fluxes_df(ecoli_core)

## End(Not run)

maxconway/fbar documentation built on Sept. 8, 2020, 6:20 p.m.