BacArena (version 1.0.1)

getPhenotype: Function to extract the phenotype of an organism object

Description

The generic function getPhenotype implements an identification of organism phenotypes.

Usage

getPhenotype(object, cutoff = 1e-06)
"getPhenotype"(object, cutoff = 1e-06)

Arguments

object

An object of class Organisms.

cutoff

A number giving the cutoff value by which value of objective function is considered greater than 0.

Value

Returns the phenotype of the organisms where the uptake of substances is indicated by a negative and production of substances by a positive number

Details

The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages. Uptake of substances is indicated by a negative and production of substances by a positive number.

See Also

Organism-class, checkPhen and minePheno

Examples

## Not run: 
# data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
# org <- Organism(Ec_core,deathrate=0.05,
#            growthlimit=0.05,growtype="exponential") #initialize a organism
# getPhenotype(org)
# ## End(Not run)