llFBA: looplessFBA

In sybilcycleFreeFlux: Cycle-Free Flux Balance Analysis (CycleFreeFlux)

Description

implements loopless FBA as described in Schellenberger et al 2011 algorithm.

Usage

llFBA(model, lpdir = SYBIL_SETTINGS("OPT_DIRECTION"), solver = SYBIL_SETTINGS("SOLVER"),
   method = SYBIL_SETTINGS("METHOD"), solverParm = data.frame(CPX_PARAM_EPRHS = 1e-07),
  verboseMode = 2)

Arguments

model	An object of class modelorg.
lpdir	Character value, direction of optimisation. Can be set to "min" or "max". Default: SYBIL_SETTINGS("OPT_DIRECTION").
solver	Single character value. The solver to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").
method	Single character value. The optimization algorithm to use. Possible values depend on the setting in solver. See SYBIL_SETTINGS for possible values. Default: LP_METHOD(SYBIL_SETTINGS).
solverParm	additional parameters to the solver
verboseMode	level of output messages

Value

status returned from the solver, objective value, and the fluxes returned from solver.

Author(s)

Abdelmoneim Amer Desouki

References

Schellenberger J, Lewis NE, Palsson BO (2011) Elimination of thermodynamically infeasible loops in steadystate metabolic models. Biophysical journal 100: 544 53

See Also

modelorg cfFBA

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.
library(sybilcycleFreeFlux)
data(Ec_core)
model=Ec_core
llFBA(model,solver="glpkAPI",verbose=2)

## The function is currently defined as
"llFBA"

sybilcycleFreeFlux documentation built on Jan. 16, 2021, 5:35 p.m.