sybil (version 1.0.1)

doubleFluxDel: Double Flux Deletion Experiment

Description

Sets every pairwise combination of fluxes in a model for one time to zero.

Usage

doubleFluxDel(model, react1, react2, allComb = FALSE,
                lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
                solver = SYBIL_SETTINGS("SOLVER"),
                method = SYBIL_SETTINGS("METHOD"),
                fld = FALSE, exex = FALSE, ...)

Arguments

model

An object of class modelorg.

react1

An object of class reactId or character or integer, fluxes set to zero (upper and lower bound) (default: react_id(model)).

react2

An object of class reactId or character or integer, fluxes set to zero (upper and lower bound) (default: react_id(model)).

allComb

Logical: If set to TRUE, all possible pairwise combinations of react1 and react2 were deleted. If set to FALSE, react1 and react2 must have the same length. Every pair c(react1[i], react2[i]) will be deleted (default: FALSE).

lpdir

Direction of optimization (default: max).

solver

The linear problem solver (default: glpk).

method

The method for the linear problem solver (default: simplex).

fld

Logical: If set to TRUE, the flux distribution for each optimization step will be stored. This increases the running time significantly (default: FALSE).

exex

Logical: exclude exchange reactions (default: FALSE).

...

Further arguments passed to optimizer.

Value

• An object of class optsol_doublefluxdel.

encoding

utf8

Details

The function doubleFluxDel studies the effect of deletion of pairs of fluxes on the current objective function (e.g. biomass production). The first step is the calculation of a reference solution, which is the wild type solution. Then n further optimisations are performed (n: number of required optimizations) with $v_i = 0$ for $i = 1,\dots,n$.

See Also

modelorg, optsol, optsol_doublefluxdel, checkOptSol, optimizer and SYBIL_SETTINGS.

Examples

data(Ec_core)
  Ec_ofd <- doubleFluxDel(Ec_core)