BacArena: getPhenotype – R documentation

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BacArena

getPhenotype

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