sybil (version 1.0.2)

oneGeneDel: One Gene Deletion Experiment

Description

Sets every set of fluxes corresponding to a gene for one time to zero.

Usage

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

Arguments

model

An object of class modelorg.

geneList

A character vector containing the set of genes to be deleted. If the argument is missing, geneList is set to allGenes(model).

lpdir

A single character value giving the direction of optimization, can be "max" for maximization or "min" for minimization. Default: lpdir = SYBIL_SETTINGS("OPT_DIRECTION").

solver

A single character value mentioning the desired optimization software, can be "glpk", "cplex" or "clp". Default: lpdir = SYBIL_SETTINGS("SOLVER").

method

A single character value giving the algorithm the optimization software mentioned in solver should use. Default: lpdir = SYBIL_SETTINGS("METHOD").

fld

Logical: If set to TRUE, the flux distribution for each optimization step will be stored in the solution object. Default: FALSE.

...

Further arguments passed to optimizer. Important ones are alg or solverParm in order to set parameter values for the optimization software.

Value

• An object of class optsol_genedel.

encoding

utf8

Details

The function ondFluxDel studies the effect of deletion of a single gene 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)