sybil (version 1.0.2)

oneFluxDel: One Flux Deletion Experiment

Description

Sets every flux in a model for one time to zero. The following optimizations were performed:

rl{ maximize $c^T \times v$ subject to $Sv = b$ $lb \le v_j \le ub$, $j = 0,\dots,i-1,i+1,\dots,n$ $v_i = 0$ }

Usage

oneFluxDel(model, react, lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
             solver = SYBIL_SETTINGS("SOLVER"),
             method = SYBIL_SETTINGS("METHOD"),
             fld = FALSE, ...)

Arguments

model

An object of class modelorg.

react

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

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).

...

Further arguments passed to optimizer.

Value

• An object of class optsol_fluxdel.

encoding

utf8

Details

The function oneFluxDel studies the effect of deletion of a single flux 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 fluxes) with $v_i = 0$ for $i = 1,\dots,n$.

See Also

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

Examples

data(Ec_core)
  Ec_ofd <- oneFluxDel(Ec_core)