cfFVA: cycle free flux variability

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

Description

finds flux variability without loops. Maximize individual reactions and test if loop exists using cfFBA. Then breaks the loop by setting the fluxes that goes to zero in loopless flux to zero.

Usage

cfFVA(model, rxnList, solver = SYBIL_SETTINGS("SOLVER"),pct_objective=100
				  ,solverParm=NA
				  ,verboseMode = 2,includeRxnEqn=TRUE
				  ,boundFlg=FALSE  
	)

Arguments

model	An object of class modelorg.
rxnList	a character vector of reaction ID's to find their flux variability
solver	Single character value. The solver to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").
pct_objective	percentage of maximum biomass to be achieved.
solverParm	extra parameters to solver, like tolerance.
includeRxnEqn	when true (default) the reaction equation is returned.
verboseMode	level of displaying messages.
boundFlg	should be set to FALSE to enumrateCycles.

Value

return two lists res and maxFlx. The first list contains reactions with the computed values. The second list contains the details of calculations. If a reaction is involved in a loop it will appear at least twice in the second list.

Author(s)

Abdelmoneim Amer Desouki

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

fva=cfFVA(model,react_id(model))
#write.csv(file="cfFVA1_cnd_res.csv",fva[[1]]);
#write.csv(file="cfFVA1_cnd_det.csv",fva[[2]]);
#plot fluxes

## The function is currently defined as
"cfFVA"

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