Function for investigating a specific phenotype of an organism
The generic function statPheno
provides statistical and visual information about a certain phenotype.
statPheno(object, type_nr = 1, phenotype_nr, dict = NULL) ## S4 method for signature 'Eval' statPheno(object, type_nr = 1, phenotype_nr, dict = NULL)
object |
An object of class Eval. |
type_nr |
A number indicating the Organism type of the phenotype to be investigated (from orgdat) |
phenotype_nr |
A number indicating the phenotype to be investigated (from orgdat) |
dict |
A character vector of all substance IDs with names that should be used instead of possibly cryptic IDs |
The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.
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) statPheno(eval, type_nr=1, phenotype_nr=2)
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