getccFBA_mat: getccFBA_mat: get ccFBA model as a constraint matrix

In sybilccFBA: Cost Constrained Flux Balance Analysis (ccFBA): MetabOlic Modeling with ENzyme kineTics (MOMENT)

Description

given Kcat vector (in 1/Sec), and molecular weights and optionally protein complex stoichiometry formulate a ccFBA problem(Maximize biomass). Improvements over MOMENT: 1- use multifunctioning enzyme constraint. 2-use one enzyme (the cheapest) for each reaction catalayzed my multiple isoenzymes and thus eliminate under estimation of rules of form ((A AND B) OR (A AND C)) 3-optionally include protein complex stoichiometry

Usage

getccFBA_mat(model, mod2 = NULL, Kcat, MW = NULL, selected_rxns = NULL, verboseMode = 2,
objVal = NULL, RHS = NULL, solver = SYBIL_SETTINGS("SOLVER"), medval = NULL, 
cpx_stoich = NULL, C_mu_coef = 0)

Arguments

model	An object of class modelorg.
mod2	An object of class modelorg with only irreversible reactions. It can be sent to save time of recalculating it with each call.
Kcat	kcat values in unit 1/S. Contains three slots: reaction id,direction(dirxn),value(val)
MW	list of molecular weights of all genes, using function calc_MW, in units g/mol
selected_rxns	optional parameter used to select a set of reactions not all, list of react_id
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. Default: 2.
RHS	the budget C, for EColi 0.27
objVal	when not null the problem will be to find the minimum budget that give the specified objective value(biomass)
solver	Single character string giving the solver package to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").
medval	median of Kcat values , used for missing values
cpx_stoich	giving the stoichiometry of complexes: data frame containing at least two columns 'genes','stoich' 'gene' : delimited string of genes(ordered by geneid(e.g bnumber)), 'stoich': number of subunits of each gene in the same order in 'genes' Default: NULL (e.g. all stoichiometry coefficients equal one)
C_mu_coef	used to have C as a linear function of mu (biomass) : C = RHS + C_mu_coef*Biomass default 0 (e.g. ignored).

Details

variable names: g1_x_1: indicates that gene x is in one-to-one relation gr_x_r:indicates that gene x catalyzes more than one reaction and this variable is the portion that catalyzes reaction r. gmr_x_cnt: variable for a gene catalyzing more than one reaction (i.e cnt reactions) and this variable is the sum of individual parts. cpx_r: used to represent a complex catalyzing reaction r.

Value

return a LIST,

LHS	constraint matrix, consists of S matrix and ccFBA constraints
rlb,rub	bounds for constraints (i.e rows)
clb,cub	bounds for variables (i.e columns)
rxnkcatRow	mapping of Kcat values to constraints
rgst	complex stoichiometry as returned by getGpr1iso
rxnGeneCol	rxn_id,gene,Col : used to get MCrowding
geneCol	low level structure, used for debugging
mod_objc_ind	row index of constraint on FBA model objective
cc_ind	capacity constraint index

Author(s)

Abdelmoneim Amer Desouki

References

Desouki, Abdelmoneim. "Algorithms for improving the predictive power of flux balance analysis." PhD diss., 2016.

See Also

getGpr1iso, cfba_moment_mr,simulate_EColi

sybilccFBA documentation built on Dec. 16, 2019, 1:34 a.m.