Function for getting a matrix of phenotypes from the dataset
The generic function getPhenoMat reconstructs a matrix with the usage of exchange reactions of the different organisms in the environment.
getPhenoMat(object, time = "total", sparse = F) ## S4 method for signature 'Eval' getPhenoMat(object, time = "total", sparse = F)
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 |
The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.
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.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.