sybil: modelorg2ExPA – R documentation

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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[i,j] of the stoichiometric matrix is treated as non-zero, if S[i,j] > tol is true. Default: `"expa"`.

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.

Value

Returns TRUE invisibly on success.

Author(s)

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

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

References

Bell, S. L. and Palsson, B. Ø. (2005) Expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 21, 1739–1740.

sybil

Efficient Constrained Based Modelling

v2.1.5

GPL-3 | file LICENSE

Authors

Mayo Roettger [cre], Gabriel Gelius-Dietrich [aut], C. Jonathan Fritzemeier [ctb], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb], Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb], Martin J. Lercher [ctb]

Initial release

2019-03-07