cfFBA: cycle free flux

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

Description

finds a cycle free flux distribution given a flux distribution and a network model.

Usage

cfFBA(model, wtflux, objVal = NA #min objval
	,fixExchRxn=TRUE
	,excReactPos=NULL
	 ,lpdir = SYBIL_SETTINGS("OPT_DIRECTION")
	 ,solver = SYBIL_SETTINGS("SOLVER")
         ,method = SYBIL_SETTINGS("METHOD")
		 ,tol=SYBIL_SETTINGS("TOLERANCE")
         ,solverParm=NA
		,verboseMode = 2
		,safeBounds=FALSE # 
######### ADDED BY GABRIEL ###############
		,retOptSol = TRUE)

Arguments

model	An object of class modelorg.
wtflux	initial flux distribution that may contain loops.
objVal	value of the objective function.
fixExchRxn	a logical value default is true, which indicates that the exchange reactions should be fixed or not.
excReactPos	list of the exchange reactions that can be sent to avoid recalculation
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
tol	tolerance of resulting solution
safeBounds	can be used to deal with false infeasibility state returned by solvers
verboseMode	level of displaying messages.
retOptSol	If set to TRUE, the function returns an object of class optsol_optimizeProb, otherwise a list.

Value

return a list that contains the status of the solution , the objective value and the fluxes that are free of cycles.

Author(s)

Abdelmoneim Amer Desouki

References

Desouki, Abdelmoneim Amer, et al. "CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions." Bioinformatics 31.13 (2015): 2159-2165.

See Also

modelorg

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.
data(iAF1260)
model=iAF1260
fba=optimizeProb(model)
cfopt=cfFBA(model,wtflux=getFluxDist(fba),objVal=lp_obj(fba), retOptSol=FALSE)
llflx=cfopt$fluxes
flx=getFluxDist(fba)
## Not run: 
layout(matrix(c(1,2,3,1,2,3), 2, 3, byrow = TRUE))
hist(log10(abs(flx[abs(llflx-flx)>1e-3])),main="loop flux",col="lightblue")
hist(log10(abs(llflx[abs(llflx-flx)>1e-3])),main="after removing loops",col="orange")
hist(log10(abs(flx[abs(llflx-flx)<1e-3])),main="fluxes not in loops",col="lightgreen")

## End(Not run)
## The function is currently defined as
"cfFBA"

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