rescue: Rescue a model

In metaboGSE: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data

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

data(Ec_core)
rescue(Ec_core, target=0.1)

metaboGSE documentation built on Oct. 23, 2020, 8:14 p.m.