getPhenoMat {BacArena} R Documentation

## Function for getting a matrix of phenotypes from the dataset

### Description

The generic function getPhenoMat reconstructs a matrix with the usage of exchange reactions of the different organisms in the environment.

### Usage

getPhenoMat(object, time = "total", sparse = F)

## S4 method for signature 'Eval'
getPhenoMat(object, time = "total", sparse = F)


### Arguments

 object An object of class Eval. time An integer indicating the time step to be used (default value is character "total") sparse A boolean indicating whether zero entries should be removed from return matrix

### Details

The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.

### Value

Returns a matrix with different phenotypes of the organism as rows and all possible exchange reactions as columns. A value of 1 means secretion, 2 means uptake and 0 means no usage of the substance of interest.

Eval-class and getPhenotype

### Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05,
minweight=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment