sybil: printReaction-methods – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

sybil

printReaction-methods

Print Columns of the Stoichiometric Matrix

Description

Print the columns of the stoichiometric matrix.

Usage

## S4 method for signature 'modelorg,ANY'
printReaction(object, react, printOut = TRUE, ...)
## S4 method for signature 'summaryOptsol,modelorg'
printReaction(object, mod, j, ...)
## S4 method for signature 'react,ANY'
printReaction(object, printOut = TRUE, ...)

Arguments

`object`	An object of class `modelorg` or of class `summaryOptsol`.
`mod`	An object of class `modelorg`.
`react`	A numeric of character vector or an object of class `reactId` containing the reaction id's of reactions to print out.
`j`	A numeric of character vector indicating the simulations to consider, see Details.
`printOut`	A single Boolean value. If set to `TRUE`, the desired reactions will be printed via the `cat` function. Default: `TRUE`.
`...`	Further arguments passed to `cat`, e.g. argument `file`.

Details

The output of the modelorg method is compatible to the file format produced by modelorg2tsv. Two columns are used: "abbreviation" containing the reaction id's and "equation" containing the reaction equation.

The summaryOptsol method prints the limiting reactions generated in simulations and stored in objects of class summaryOptsol. Slot react_id of class summaryOptsol contains a list of reaction id's: list element j gives the reaction id's limiting simulation number j.

Value

The modelorg method returns invisibly a character vector of length equal to the number of reactions given in argument react. Each string consists of two tab-delimited values: first, the reaction id, second, the reaction equation.

The summaryOptsol returns invisibly a list of length equal to the number of elements in argument j. Each list element is of the same type as the return value of the modelorg method.

Methods

signature(object = "modelorg"): method to use with objects of class modelorg.
signature(object = "summaryOptsol", mod = "modelorg"): method to use with objects of class summaryOptsol.
signature(object = "react", ...): method to use with objects of class react.

Author(s)

Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>

Maintainer: Mayo Roettger <mayo.roettger@hhu.de>