metaboGSE (version 1.2.5)

rescue: Rescue a model

Description

The function rescues a given model.

Usage

rescue(
  model,
  target,
  react = NULL,
  weight.type = "r",
  timeout = 12,
  prefix.rescue = NA,
  prefix.rescued = NA,
  rescue.threshold = 1e-05
)

Arguments

model

An object of class modelorg.

target

A numeric vector for growth target.

react

A numeric vector or a character vector containing reaction id's. Default: reactions in objective function.

weight.type

A character indicating which type of weighting to use in model objective modification, i: 1, r: 1/coefficient, s: 1/sqrt(coefficient). Default: r.

timeout

The maximum time in seconds to allow for LP call to return. Default: 12.

prefix.rescue

A string indicating the prefix of output rescue model. Default: no output.

prefix.rescued

A string indicating the prefix of output rescued model. Default: no output.

rescue.threshold

A numeric value indicating the threshold to consider a rescue. Default: 1e-5.

Value

The rescue and rescued models, as well as the coefficient set to rescue reactions. SYBIL_SETTINGS("OPT_DIRECTION") is set to "min".

Examples

# NOT RUN {
data(Ec_core)
rescue(Ec_core, target=0.1)
# }