Class "netFlux"
Class "netFlux" groups exchange reaction rates according to their sign
in uptake, excretion and unused reactions.
Objects can be created by calls of the form getNetFlux(rates, tol),
with argument rates being a named numeric vector containing reaction
rates of exchange fluxes and corresponding reaction id's. Argument
rates can be obtained by a call to optimizeProb. The
second argument tol is a tolerance value (default:
SYBIL_SETTINGS("TOLERANCE")). Reaction rates less than tol * -1
are uptake reactions, reaction rates greater than tol are excretion
reactions and all others (abs(rates) < tol) are unused reactions.
uptake:Object of class "logical" indicating uptake reactions.
product:Object of class "logical" indicating excretion reactions.
unused:Object of class "logical" indicating unused reactions.
react_id:Object of class "character" containing the reaction id's of the
exchange reactions.
rate:Object of class "numeric" containing the reaction rates of the
exchange reactions.
signature(x = "netFlux"):
number of exchange reactions.
signature(object = "netFlux"):
gets the rate slot.
signature(object = "netFlux"):
gets the react_id slot.
signature(object = "netFlux"):
sets the react_id slot.
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
data(Ec_core) # retrieve all exchange reactions ex <- findExchReact(Ec_core) # perform flux balance analysis opt <- optimizeProb(Ec_core, algorithm = "fba") # get flux distribution of all exchange reactions fd <- getFluxDist(opt, ex) # group exchange reactions getNetFlux(fd)
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