Constructor of the S4 class Organism-class
Constructor of the S4 class Organism-class
Organism( model, algo = "fba", ex = "EX_", ex_comp = NA, csuffix = "\\[c\\]", esuffix = "\\[e\\]", lyse = FALSE, feat = list(), typename = NA, setExInf = TRUE, setAllExInf = FALSE, coupling_constraints = list(), predator = "", ... )
model |
Object of class sybil::modelorg containging the genome sclae metabolic model |
algo |
A single character string giving the name of the algorithm to use. See SYBIL_SETTINGS |
ex |
Identifier for exchange reactions |
ex_comp |
Defining exchange reactions whose compounds should be added to the medium of the arena (default: all) |
csuffix |
suffix for intern metabolites used by lysis function. |
esuffix |
suffix for external metabolites used by lysis function. |
lyse |
A boolean variable indicating if the organism should lyse after death. |
feat |
A list containing conditional features for the object (contains at the momement only biomass components for lysis). |
typename |
A string defining the name (set to model name in default case) |
setExInf |
Enable if all lower bounds of exchange reaction which are set to zero (i.e. no uptake possible!) should be set to -infitity (default: true) |
setAllExInf |
Enable if all lower bounds of exchange reaction should be set to -infitity (default: false) |
coupling_constraints |
List with coupling parameters. |
predator |
Name of organism which can kill this one. |
... |
Arguments of |
Object of class Organism
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