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geneDeletion
studies the effect of in sillico gene
deletions on the current objective function (e.g. biomass production).geneDeletion(model, genes, combinations = 1, ...)
modelorg
.combinations > 1
and genes
is not a
matrix, combinations
is the number of elements from genes
taken at a time while building all combinations of the elements in
optimizer
.optsol_genedel
.genes
is a matrix of character values (gene id's) or
integers (pointers to gene id's), each column is treated as one deletion
experiment. If the matrix is made up of integers, a zero entry means no gene.
If argument genes
is a character vector or integer, the argument
combinations
gives the number of gene id's taken each time in order
to build all possible combinations of genes
. A matrix is constructed
using combn
.
If argument genes
is empty, the number of unique genes in model
is used.modelorg
, optsol
,
optsol_genedel
,
checkOptSol
, oneGeneDel
,
optimizer
, optimizeProb
,
combn
and SYBIL_SETTINGS
.## load the dataset
data(Ec_core)
## perform a single gene deletion analysis (delete every gene one time)
gd <- geneDeletion(Ec_core)
## triple gene deletion analysis using the first ten genes
gd <- geneDeletion(Ec_core, genes = 10, combinations = 3)
## perform a double gene deletion analysis (delete all possible pairwise
## combinations of all genes)
gd <- geneDeletion(Ec_core, combinations = 2)
## perform a triple gene deletion analysis
## (very high number of optimizations)
gd <- geneDeletion(Ec_core, combinations = 3)
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