find_flux_variability_df

a data frame representing the metabolic model

reaction_table

number of times to calculate fluxes

folds

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

do_minimization

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

A toolkit for Flux Balance Analysis and related
metabolic modeling techniques. Functions are provided for: parsing
models in tabular format, converting parsed metabolic models to input
formats for common linear programming solvers, and
evaluating and applying gene-protein-reaction mappings. In addition, there
are wrappers to parse a model, select a solver, find the metabolic fluxes,
and return the results applied to the original model. Compared to other
packages in this field, this package puts a much heavier focus on
providing reusable components that can be used in the design of new
implementation of new techniques, in particular those that involve large
parameter sweeps. For a background on the theory, see What is Flux Balance
Analysis <doi:10.1038/nbt.1614>.

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

Description

Usage

Arguments

Value

Details