Description Usage Arguments Value Author(s) See Also Examples
View source: R/findFluxGeneExpr.R
given a flux distribution, use gpr to formulate a MILP to find minimal set of required genes such that any GPR rule of a reaction carrying a nonzero flux must be evaluated to TRUE.
1 2 3 4 | findFluxGeneExpr(model, fluxes, threshold = 1e-06,
lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
solver = SYBIL_SETTINGS("SOLVER"), method = SYBIL_SETTINGS("METHOD"),
solverParm = SYBIL_SETTINGS("SOLVER_CTRL_PARM"), verboseMode = 2)
|
model |
An object of class |
fluxes |
The flux distribution that we want to find the minimal set of genes able to produce it. |
threshold |
Threshold in flux default value 1e-6. Fluxes with magnitude less than threshold are considered zeros. |
lpdir |
Character value, direction of optimisation. Can be set to |
solver |
Single character value. The solver to use. See
|
method |
Single character value. The optimization algorithm to use. Possible values
depend on the setting in |
solverParm |
A data frame containing parameters for the specified solver. |
verboseMode |
An integer value indicating the amount of output to stdout:
0: nothing, 1: status messages, 2: like 1 plus with more details,
3: generates files of the LP problem. |
return list of genes with State: "ON" if it is required, "OFF": when it is not required.
Abdelmoneim Amer Desouki
modelorg
,
optimizeProb
,
eFBA_gene
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ## Not run:
data(iAF1260)
model=iAF1260
allgenes=allGenes(model)
exoff=cbind(LOCUS=allgenes,State=rep(0,length(allgenes)));
testgpr=(gpr(model)!="")
table(testgpr)
slvr="glpkAPI"
seroff = eFBA_gene(model, exoff,solver=slvr,verbose=3,
testgpr=testgpr,Tf=0.0001)
mnflx=optimizeProb(model, algorithm = "mtf",solver=slvr);
sfba=optimizeProb(model,solver=slvr)
eFBAg_flx=seroff$rxn[, "newFlux"]
geFBA=findFluxGeneExpr(model,fluxes(sfba)[fldind(sfba)],
threshold=0.0001,verboseMode=4)
gemnFBA=findFluxGeneExpr(model,fluxes(mnflx)[fldind(mnflx)],
threshold=0.0001,verboseMode=4)
geEFBAg=findFluxGeneExpr(model,as.numeric(seroff$rxn[, "newFlux"]),
threshold=0.0001,verboseMode=4)
# The minimum number of genes required to get each of the three fluxes
print(cbind(EFBA_reqGenes=sum(geEFBAg$State=="ON"),
minTotFlx_reqGene=sum(gemnFBA$State=="ON"),
FBA_reqGenes=sum(geFBA$State=="ON")) )
## End(Not run)
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