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

Description Usage Arguments Value

Description

Constructor of the S4 class Organism-class

Usage

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

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

ex_comp

csuffix

csuffix

esuffix

esuffix

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

...

Arguments of Organism-class

Value

Object of class Organism


BacArena documentation built on May 24, 2017, 1:02 a.m.

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