sybil (version 2.0.0)

doubleGeneDel: Double Gene Deletion Experiment

Description

Predict the metabolic phenotype of of double-gene knock out mutants.

Usage

doubleGeneDel(model, geneList1, geneList2, lb = NULL, ub = NULL,
                allComb = FALSE, exLethal = TRUE,
                tol = SYBIL_SETTINGS("TOLERANCE"),
                checkOptSolObj = FALSE, ...)

Arguments

model

An object of class '>modelorg.

geneList1

A character vector containing the set of genes to be deleted. Default: allGenes(model).

geneList2

A character vector containing the set of genes to be deleted. Default: allGenes(model).

lb

A numeric vector containing the lower bounds for the reaction rates of reactions (variables) affected by the genes given in arguments geneList1 and geneList2. If set to NULL, all reactions affected will be constrained to zero. Default: NULL.

ub

A numeric vector containing the upper bounds for the reaction rates of reactions (variables) affected by the genes given in arguments geneList1 and geneList2. If set to NULL, all reactions affected will be constrained to zero. Default: NULL.

allComb

A single Boolean value. If set to TRUE, every possible pairwise combination of genes given in arguments geneList1 and geneList2 will be knocked-out. If set to FALSE, arguments geneList1 and geneList2 must have the same length. The knock-outs will be computed pair-wise: first geneList1[1] and geneList2[1], second geneList1[2] and geneList2[2] and so on. Default: FALSE.

exLethal

A single Boolean value. If set to TRUE, lethal genes are removed from the analysis. A unique set of genes in geneList1 and geneList2 will be scanned for lethal genes. A particular gene \(i\) is considered as lethal, if the deletion of this gene results in a zero flux rate in the objective function given in model. Default: TRUE.

tol

A single numeric value, containing an absolute threshold value for a gene being lethal or not. Default: SYBIL_SETTINGS("TOLERANCE").

checkOptSolObj

A single logical value. If set to TRUE, a warning will be generated, if not all optimizations ended successful. Default: FALSE.

…

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

Value

An object of class '>optsol_genedel.

Details

The function doubleGeneDel studies the effect of genetic perturbations by double gene deletions on the phenotype of the metabolic network. The function performs \(n\) optimizations with \(n\) being either the length of the character vector in argument geneList1 times the length of the character vector in argument geneList2, if argument allComb is set to TRUE, or the length of one of these vectors if argument allComb is set to FALSE. For each gene deletion \(i,j\) the set of fluxes effected by the simultaneous deletion of genes \(i\) and \(j\) is constrained to zero flux. If the deletion of a certain pair of genes has an effect, is tested with the function geneDel. Each optimization corresponds to the simultaneous deletion of two genes.

See Also

modelorg, '>optsol, '>optsol_genedel, checkOptSol, optimizer and SYBIL_SETTINGS.

Examples

# NOT RUN {
  ## compute all possible pairwise gene deletions
  # load example data set
  data(Ec_core)
  
  # compute all possible pairwise gene deletions via
  # FBA (default)
  Ec_dgd <- doubleGeneDel(Ec_core, allComb = TRUE)
  
  # or MOMA (linearized version)
  Ec_dgd <- doubleGeneDel(Ec_core,
                          allComb = TRUE,
                          algorithm = "lmoma")
# }