getPhenotype: Function to extract the phenotype of an organism object

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

Function to extract the phenotype of an organism object

Description

The generic function getPhenotype implements an identification of organism phenotypes.

Usage

getPhenotype(object, cutoff = 1e-06, fbasol, par = FALSE)

## S4 method for signature 'Organism'
getPhenotype(object, cutoff = 1e-06, fbasol, par = FALSE)

Arguments

object	An object of class Organisms.
cutoff	A number giving the cutoff value by which value of objective function is considered greater than 0.
fbasol	Problem object according to the constraints and then solved with optimizeProb.
par	A boolean indicating if running in parallel mode.

Details

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

Value

Returns the phenotype of the organisms where the uptake of substances is indicated by a negative and production of substances by a positive number

See Also

Organism-class, checkPhen and minePheno

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