This function removes specified genes from a model, and optionally also reactions and metabolites inaccessible after gene knock outs.
Arguments
- model
Model of class ModelOrg
- gene
A character vector stating the reaction IDs in a model or a numeric vector providing the reaction indices.
- rm_react
Logical. Should reaction, which are inaccessible after the gene knock outs, be deleted as well?
- rm_met
Logical. Should metabolites, which are singletons after the reaction removal, be deleted as well?
Value
An updated model of class ModelOrg
Examples
fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)
mod
#> model ID: e_coli_core
#> model name: e_coli_core
#> number of compartments: 2
#> e ( extracellular space )
#> c ( cytosol )
#> number of reactions: 95
#> number of metabolites: 72
#> number of unique genes: 137
#> number of user constraints: 0
#> number of subsystems: 0
#>
#> objective function: +1 BIOMASS_Ecoli_core_w_GAM
#> objective direction: maximize
# create a double gene knock-out mutant
mod_KO <- rmGene(mod, c("b4152","b0116"))
mod_KO
#> model ID: e_coli_core
#> model name: e_coli_core
#> number of compartments: 2
#> e ( extracellular space )
#> c ( cytosol )
#> number of reactions: 92
#> number of metabolites: 72
#> number of unique genes: 135
#> number of user constraints: 0
#> number of subsystems: 0
#>
#> objective function: +1 BIOMASS_Ecoli_core_w_GAM
#> objective direction: maximize