getPhenotype {BacArena}R Documentation

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


[Package BacArena version 1.8.2 Index]