statPheno: Function for investigating a specific phenotype of an...

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

Function for investigating a specific phenotype of an organism

Description

The generic function statPheno provides statistical and visual information about a certain phenotype.

Usage

statPheno(object, type_nr = 1, phenotype_nr, dict = NULL)

## S4 method for signature 'Eval'
statPheno(object, type_nr = 1, phenotype_nr, dict = NULL)

Arguments

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

Details

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

See Also

Eval-class

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)
statPheno(eval, type_nr=1, phenotype_nr=2)

euba/BacArena documentation built on Aug. 29, 2024, 11:15 p.m.