Organism-constructor: Constructor of the S4 class 'Organism-class'

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

Constructor of the S4 class Organism-class

Description

Constructor of the S4 class Organism-class

Usage

Organism(
  model,
  algo = "fba",
  ex = "EX_",
  ex_comp = NA,
  csuffix = "\\[c\\]",
  esuffix = "\\[e\\]",
  lyse = FALSE,
  feat = list(),
  typename = NA,
  setExInf = TRUE,
  setAllExInf = TRUE,
  coupling_constraints = list(),
  predator = "",
  ...
)

Arguments

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: true). Set this to FALSE in case you want to use the constraints that are instrinsically set in your input model.
coupling_constraints	List with coupling parameters.
predator	Name of organism which can kill this one.
...	Arguments of Organism-class

Value

Object of class Organism

euba/BacArena documentation built on Aug. 29, 2024, 11:15 p.m.