sybilcycleFreeFlux (version 2.0.2)

cfFVA: cycle free flux variability

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.

See Also

modelorg cfFBA

Examples

# NOT RUN {
##---- 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"
# }