Double Gene Deletion Experiment
Predict the metabolic phenotype of of double-gene knock out mutants.
doubleGeneDel(model, geneList1, geneList2, lb = NULL, ub = NULL,
allComb = FALSE, exLethal = TRUE,
tol = SYBIL_SETTINGS("TOLERANCE"),
checkOptSolObj = FALSE, ...)model |
An object of class |
geneList1 |
A character vector containing the set of genes to be deleted. |
geneList2 |
A character vector containing the set of genes to be deleted. |
lb |
A numeric vector containing the lower bounds for the reaction rates of
reactions (variables) affected by the genes given in arguments
|
ub |
A numeric vector containing the upper bounds for the reaction rates of
reactions (variables) affected by the genes given in arguments
|
allComb |
A single Boolean value. If set to |
exLethal |
A single Boolean value. If set to |
tol |
A single numeric value, containing an absolute threshold value for a gene
being lethal or not. |
checkOptSolObj |
A single logical value. If set to |
... |
Further arguments passed to |
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.
An object of class optsol_genedel.
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
## 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")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.