getPhenoMat: Function for getting a matrix of phenotypes from the dataset

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

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.

See Also

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
arena <- addOrg(arena,bac,amount=10) #add 10 organisms
arena <- addSubs(arena,40) #add all possible substances
eval <- simEnv(arena,5)
phenmat <- getPhenoMat(eval)

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