pfba: Maximizes a set of given fluxes within the k-cone using...

Description Usage Arguments Value Examples

View source: R/linprog.R

Description

Maximizes a set of given fluxes within the k-cone using parsimonous FBA. Here, 'parsimonous' means that from all the possible maxima we will return the one minimizing the overall flux sum, thus, being the most 'economic' one for the organism.

Usage

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pfba(obj, S, alpha = 1, v_min = 0, v_max = 1)

Arguments

obj

The objective reaction, whose flux will be be maximized. Can be any of the following three:

  • A list containing at least the four vectors S, P, N_S, and N_P, which which contain the names of substrates and products and their respective stochiometries.

  • A unnamed vector containing the corresponding column in the stochiometric matrix.

  • A named vector containing only the non-zero entries in the respective column of the stochiometric matrix being named by their respective metabolite.

  • A single integer indicating which column of the stoichiometric contains the objective reaction.

S

The stochiometrix matrix to be used (must be irreversible).

alpha

Fraction of optimum value. Objective must be at least alpha * fba_solution.

v_min

Lower bounds for the reaction fluxes. Can be a single value or a vector containing one value for each reaction.

v_max

Upper bounds for the reaction fluxes. Can be a single value or a vector containing one value for each reaction.

Value

A vector with the same length as columns in S containing the solution of the optimization.

Examples

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S <- matrix(c(1, 0, -2, 1), ncol = 2)
rownames(S) <- c("A", "B")
pfba(c(B = -1), S)

cdiener/dycone documentation built on Sept. 9, 2018, 1:20 p.m.