findRxnFlux: Function to get all reactions fluxes that are associated with...

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

Function to get all reactions fluxes that are associated with the metabolite of a given exchange reactions

Description

The generic function findRxnFlux returns a matrix with the flux for each organism and the reaction that is using the metabolite of the given exchange reaction

Usage

findRxnFlux(object, ex, time, print_reactions = FALSE, drop_unused = TRUE)

## S4 method for signature 'Eval'
findRxnFlux(object, ex, time, print_reactions = FALSE, drop_unused = TRUE)

Arguments

object	An object of class Eval.
ex	An exchange reaction of which the metabolite should be shared for in all reactions
time	the time point of the simulation which should be considered
print_reactions	If true the detailed definition of each reactions is printed
drop_unused	If true then inactive reactions will be excluded

Details

Returns a list with the minimum and maximum substance usage for each time point.

See Also

Eval-class and simEnv

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)
fluxlist <- findRxnFlux(eval, "EX_h(e)", 5)

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