ACHR: Random Sampling of Solution Space

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

Description

implements sampling algorithm

Usage

ACHR(model, W = 2000, nPoints = 5000, stepsPerPoint = 10, 
solver = SYBIL_SETTINGS("SOLVER"), method = SYBIL_SETTINGS("METHOD"))

Arguments

model	An object of class modelorg.
W	Number of warmup points. It should be more than double the number of reactions of the model.
nPoints	Number of points to be generated
stepsPerPoint	number of steps per point, default is 10 steps.
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).

Details

Starts by calculating warm up points

Author(s)

Abdelmoneim Amer Desouki

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;
solver="cplexAPI"
W=500
nPnts=1000
s1=ACHR(model,W,nPoints=nPnts,stepsPerPoint=10)


sFVA=fluxVar(model,solver=solver) 
fva_min=sFVA@lp_obj[(c(1:length(react_id(model))))];
fva_max=sFVA@lp_obj[(c((length(react_id(model))+1):(2*length(react_id(model)))) )];
table(lp_stat(sFVA))

pnts=s1$Points
fvamin=apply(pnts,1,min)
fvamax=apply(pnts,1,max)

#write.csv(file="fva.csv",cbind(fva_min,fvamin,fva_max,fvamax,lb=lowbnd(model),
#ub=uppbnd(model)))
#####Plot samples
bmrxn=which(obj_coef(model)==1)
bmrow=S(model)[bmrxn,]

objvals=NULL
solver="glpkAPI"
nRxns=react_num(model);
llpnts=  matrix(rep(0,nRxns*nPnts),ncol=nPnts);
for(i in 1:nPnts){
	objvals=rbind(objvals,obj= pnts[bmrxn,i])
	lrf=lrFBA(model,wtflux=pnts[,i],solver=solver,objVal= pnts[bmrxn,i])
	llpnts[,i]=lrf$fluxes;
#Sys.time()
	print(sprintf("point %d:%f",i,objvals[i]))
}
llfvamin=apply(llpnts,1,min)
llfvamax=apply(llpnts,1,max)

 #write.csv(file="objv.csv",objvals)
#write.csv(file="llfva.csv",cbind(fva_min,llmin=llfvamin,fva_max,llmax=llfvamax,fvamin,
fvamax,lb=lowbnd(model),ub=uppbnd(model)))
nloopflux=NULL
loopflxll=NULL
loopflxlp=NULL

for(i in (1:length(react_id(model))))
	for(j in (1:nPnts)){
	#print(c(i,j))
		if(abs(pnts[i,j]-llpnts[i,j])<1e-7){
			nloopflux=c(nloopflux,pnts[i,j])
		}else{
		loopflxll=c(loopflxll,llpnts[i,j])
		loopflxlp=c(loopflxlp,pnts[i,j])
		}
	}
layout(matrix(c(1,2,3,1,2,3), 2, 3, byrow = TRUE))
hist(log10(abs(loopflxlp)),col="lightblue",main="a-loop fluxes",xlim=c(-3,3),
xlab="Log10(flux)")
hist(log10(abs(loopflxll)),col="orange",main="b-using cycleFreeFlux",
xlim=c(-3,3),xlab="Log10(flux)")
hist(log10(abs(nloopflux)),col="lightgreen",main="c-non-loop fluxes",
xlim=c(-3,3),xlab="Log10(flux)")


## End(Not run)

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