doubleReact: Identifies Identical Reactions
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Details Value Note Author(s) Examples

The function doubleReact identifies identical reactions (isoenzymes) in a model.

1	doubleReact(model, checkRev = TRUE, linInd = FALSE)

`model`	An object of class `modelorg`.
`checkRev`	A single logical value. If set to `TRUE`, two reactions are identical, if, additionally to the stoichiometric coefficients, the direction of the reactions is the same (the corresponding value of slot `react_rev` of the model). Default: `TRUE`.
`linInd`	A single logical value. If set to `TRUE`, two reactions are identical, if the vectors of stoichiometric coefficients are linear dependent. For example, two reactions with coefficients (1, 1, -1) and (2, 2, -2) are linear dependent. If the coefficients have different signs, for example (-1, 1) and (1, -1) (the first reaction being forward direction and the second one being backward direction), they are not identical. If `linInd` is set to `FALSE`, the stoichiometric must be identical, for two reactions considered to be identical. Default: `FALSE`.

In the first step, the stoichiometric matrix S is divided into groups of reactions containing the same number of metabolites. After that, the row indices of the non-zero elements of these matrices are compared. If identical pairs are found, we check the corresponding values in S. If they are also identical, the reversibility of the reactions are examined. If they are the same, the two reactions are called identical.

If no identical reactions were found, the return value is FALSE. Otherwise a list is returned, ordered by the number of metabolites used in each reaction. Each element is a numerical vector containing the indices (column number fo the stoichiometrix matrix) of identical reactions.

At the moment, the directions of a pair of reactions is not compared. Meaning, that if concerning to the values in S the reaction is in forward direction, but not when including the flux values, doubleReact will not find it.

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

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