doubleGeneDel: Double Gene Deletion Experiment

Description

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

Usage

doubleGeneDel(model, geneList1, geneList2, allComb = FALSE,
                lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
                solver = SYBIL_SETTINGS("SOLVER"),
                method = SYBIL_SETTINGS("METHOD"),
                fld = FALSE, exLethal = TRUE,
                tol = SYBIL_SETTINGS("TOLERANCE"), ...)

Arguments

model

An object of class modelorg.

geneList1

Character: the genes to delete (default: allGenes(model)).

geneList2

Character: the genes to delete (default: allGenes(model)).

allComb

Logical: If set to TRUE, all possible pairwise combinations of geneList1 and geneList2 were deleted. If set to FALSE, geneList1 and geneList2 must have the same length. Every pair c(geneList1[i], geneList2[i]) will be deleted

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).

exLethal

Logical: If set to TRUE, lethal genes are removed from the analysis. This increases the running time significantly (default: TRUE).

tol

Numeric: threshold value for a gene beeing lethal or not (default: 1E-6).

...

Further arguments passed to optimizer.

Value

An object of class optsol_doublegenedel.

encoding

utf8

Details

The function doubleGeneDel studies the effect of deletion of pairs of genes 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 $i = 1,\dots,n$.

Examples

Run this code

data(Ec_core)
  Ec_ofd <- doubleGeneDel(Ec_core)

Run the code above in your browser using DataLab