sybil (version 2.2.0)

doubleReact: Identifies Identical Reactions

Description

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

Usage

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

Arguments

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.

Value

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.

Details

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.

Examples

# NOT RUN {
  data(Ec_core)
  Ec_dr <- doubleReact(Ec_core)
# }