checkPhen: Function for checking phenotypes in the environment

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

Function for checking phenotypes in the environment

Description

The generic function checkPhen checks and adds the phenotypes of organisms in the environment.

Usage

checkPhen(object, org, cutoff = 1e-06, fbasol)

## S4 method for signature 'Arena'
checkPhen(object, org, cutoff = 1e-06, fbasol)

Arguments

object	An object of class Arena.
org	An object of class Organism.
cutoff	A number giving the cutoff for values of the objective function and fluxes of exchange reactions.
fbasol	Problem object according to the constraints and then solved with optimizeProb.

Details

The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages. Uptake of substances are indicated by a negative and production of substances by a positive number.

Value

Returns a number indicating the number of the phenotype in the phenotype list.

See Also

Arena-class and getPhenotype

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.