fba: Maximizes the flux through a given objective reaction.

Description Usage Arguments Value Examples

View source: R/linprog.R

Description

Maximizes the flux through a given objective reaction.

Usage

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fba(obj, S, 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).

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")
fba(c(B = -1), S)

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