Add linear reaction flux constraints to a metabolic network.
Usage
addConstraint(model, react, coeff, rtype, lb = NULL, ub = NULL)
# S4 method for class 'ModelOrg,character,numeric,character'
addConstraint(model, react, coeff, rtype, lb = NULL, ub = NULL)
# S4 method for class 'ModelOrg,list,list,character'
addConstraint(model, react, coeff, rtype, lb = NULL, ub = NULL)Arguments
- model
Model of class ModelOrg
- react
Character vector or a list of character vectors containing the model's reactions IDs that are part of the respective constraint.
- coeff
Numeric vector or list of numeric vectors defining the coefficients for the reactions listed in 'react'.
- rtype
Character vector describing the type of the constraint(s). See details.
- lb, ub
Numeric vector defining the lower and upper bound(s) of the constraint(s).
Details
The slot "rtype" describes the type of each constraint. Valid values and their effects are:
| code | description | rule |
| "F" | free constraint | \(-\infty < x < \infty\) |
| "L" | constraint with lower bound | \(lb \leq x \leq \infty\) |
| "U" | constraint with upper bound | \(-\infty \leq x \leq ub\) |
| "D" | double-bounded (ranged) constraint | \(lb \leq x \leq ub\) |
| "E" | fixed (equality constraint) | \(lb = x = ub\) |
Examples
fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)
# Simulate anaerobic growth
mod <- changeBounds(mod, "EX_o2_e", lb = 0)
# Limit the proton production depending on the growth rate
mod <- addConstraint(mod,
react = c("EX_h_e","BIOMASS_Ecoli_core_w_GAM"),
coeff = c(1, -20), rtype = "U", ub = 0)