ReDirection (version 1.0.1)

calculate_reaction_vector: calculate_reaction_vector() This is the main function of the package 'ReDirection'.

Description

The input stoichiometry matrix of a generic biochemical network is checked and modified after which the null space is computed.

Usage

calculate_reaction_vector(smat, rar)

Arguments

smat

An input stoichiometry matrix of a generic biochemical network. This is a mandatory argument.

rar

A mandatory logical argument that indicates the orientation of the reactions as rows (TRUE) or columns (FALSE) in the stoichiometry matrix.

Value

code A numerically encoded ('0', no success; '1', success) text message to the user and indicates the outcome of utilizing "ReDirection".

Details

The non-zero null space spanning and the subspace-generated unique reaction vectors (RVs) are recursively summed combinatorially and evaluated for redundancy.

The function compares the generated subspace vectors reaction-wise, i.e., as sequences of identical terms across all RVs. These are then evaluated on the basis of pre-defined criteria (descriptive statistics, linear maps, tests of convergence, probability of occurrence, vector norms).

The output for each reaction is the combined propensity (p1-norm) of the sub- propensities and is strictly positive. This is the probable rate constant, is used to infer the dominant direction of each reaction and annotate a reaction as "Forward (f)" or "Reverse (b)" or "Equivalent (e)". Although, there is no restriction on the number of reactions, the inherent computational complexity (NP-hard) involved per iteration suggests that an suitable value for the number of reactions is around 20.

Examples

# NOT RUN {
mx <- matrix(c(1,0,0,0,0,1,0,-1,0,1,0,0,1,0,0,0,-1,1,1,0,0,0,0,0,0,-2,0,-1,
-1,1,0,0,0,0,1,0,-1,1,0,0,0,0,0,0,-1,0,1,0,-1,0,0,0,0,0,-1,0,1,0,0,-1,0,-1,0)
,byrow=TRUE,nrow=9,ncol=7)
calculate_reaction_vector(mx,TRUE)

# }