BacArena (version 1.8.2)

Organism-constructor: 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 = FALSE,
  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: false)

coupling_constraints

List with coupling parameters.

predator

Name of organism which can kill this one.

...

Arguments of Organism-class

Value

Object of class Organism