modelorg2ExPA: Write an Instance of Class modelorg to File in ExPA Format

Description

The function modelorg2ExPA writes the content of an instance of class modelorg to text files in a format which can be read by the program ExPA to compute extreme pathways.

Usage

modelorg2ExPA(model, fname = NULL, exIntReact = NULL,
                filepath = ".", suffix = "expa",
                tol = SYBIL_SETTINGS("TOLERANCE"))

Arguments

model

An object of class modelorg.

fname

An single character string giving the filename to write to. Default: <model_id>.expa.

exIntReact

An object of class '>reactId, character or integer, giving id's of internal reactions to exclude in the ExPA file. Default: NULL.

filepath

A single character string giving the path to a certain directory in which the output files will be stored. Default: ".".

suffix

A single character string giving the file name extension. Default: "expa".

tol

A single numeric value giving the limit of tolerance. An element \(S_{ij}\) of the stoichiometric matrix is treated as non-zero, if \(|S_{ij}| > \textrm{tol}\) is true. Default: "expa".

Value

Returns TRUE invisibly on success.

Details

The function modelorg2ExPA produces input files for the program ExPA. With ExPA, it is possible to calculate extreme pathways in metabolic networks.

The function produces a warning, if a reaction contains non-integer stoichiometric values, because they are not compatible with the ExPA program.

References

Bell, S. L. and Palsson, B. <U+00D8>. (2005) Expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 21, 1739--1740.