netFlux-class: Class '"netFlux"'

In SysBioChalmers/sybil: Efficient Constrained Based Modelling

Class "netFlux"

Description

Class "netFlux" groups exchange reaction rates according to their sign in uptake, excretion and unused reactions.

Objects from the Class

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.

Slots

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.

Methods

length

signature(x = "netFlux"): number of exchange reactions.

rate

signature(object = "netFlux"): gets the rate slot.

react_id

signature(object = "netFlux"): gets the react_id slot.

react_id<-

signature(object = "netFlux"): sets the react_id slot.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

optimizeProb, getFluxDist

Examples

  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)

SysBioChalmers/sybil documentation built on Aug. 24, 2023, 1:08 p.m.