optsol_dynamicFBA-class: Class '"optsol_dynamicFBA"'

In sybilDynFBA: Dynamic FBA : Dynamic Flux Balance Analysis

Description

Structure of the class "optsol_dynamicFBA". Objects of that class are returned by the function dynamicFBA. Extends the Class optsol_optimizeProb.

Objects from the Class

Objects can be created by calls of the function optsol_dynamicFBA:

test <- optsol_dynamicFBA(solver = "glpk", method = "simplex").

Slots

solver:

Object of class "character" indicating the used solver.

method:

Object of class "character" indicating the used method.

num_of_prob:

Object of class "integer" indicating the number of optimization problems.

lp_num_cols:

Object of class "integer" indicating the number of columns.

lp_num_rows:

Object of class "integer" indicating the number of rows.

lp_obj:

Object of class "numeric" containing the values of the objective function.

lp_ok:

Object of class "integer" containing the exit code of the optimization.

lp_stat:

Object of class "integer" containing the solution status of the optimization.

lp_dir:

Object of class "character" indicating the direction of optimization.

concentrationMatrix

Object of class "matrix" contains concentrations of extracellular metabolite

excRxnNames

Object of class "matrix" contains names of exchange reactions for the EC metabolites

fluxdist:

Object of class "fluxDistribution" containing the solutons flux distributions.

timeVec

Object of class "numeric" Vector of time points

biomassVec

Object of class "numeric" Vector of biomass values

all_fluxes

Object of class "matrix" contains fluxes of all reactions at all steps

Extends

Class "optsol_optimizeProb", directly. Class "optsol", by class "optsol_optimizeProb", distance 2.

Methods

plot

signature(x = "optsol_dynamicFBA", y = "missing"):

x

An object of class optsol_dynamicFBA.

y

not used but kept for compitability with generic plot.

plotRxns

List of reaction id's to be ploted

...

Further arguments passed to sysBiolAlg. Argument solverParm is a good candidate.

Author(s)

Abdelmoneim Amer Desouki

See Also

checkOptSol, optsol, optsol_optimizeProb

Examples

showClass("optsol_dynamicFBA")

sybilDynFBA documentation built on July 1, 2020, 6:07 p.m.