ReDirection: Predict Dominant Direction of Reactions of a Biochemical Network

Biologically relevant, yet mathematically sound constraints are used to compute the propensity and thence infer the dominant direction of reactions of a generic biochemical network. The reactions must be unique and their number must exceed that of the reactants,i.e., reactions >= reactants + 2. 'ReDirection', computes the null space of a user-defined stoichiometry matrix. The spanning non-zero and unique reaction vectors (RVs) are combinatorially summed to generate one or more subspaces recursively. Every reaction is represented as a sequence of identical components across all RVs of a particular subspace. The terms are evaluated with (biologically relevant bounds, linear maps, tests of convergence, descriptive statistics, vector norms) and the terms are classified into forward-, reverse- and equivalent-subsets. Since, these are mutually exclusive the probability of occurrence is binary (all, 1; none, 0). The combined propensity of a reaction is the p1-norm of the sub-propensities, i.e., sum of the products of the probability and maximum numeric value of a subset (least upper bound, greatest lower bound). This, if strictly positive is the probable rate constant, is used to infer dominant direction and annotate a reaction as "Forward (f)", "Reverse (b)" or "Equivalent (e)". The inherent computational complexity (NP-hard) per iteration suggests that a suitable value for the number of reactions is around 20. Three functions comprise ReDirection. These are check_matrix() and reaction_vector() which are internal, and calculate_reaction_vector() which is external.

Version: 1.0.1
Depends: stats, MASS, pracma
Imports: gtools
Suggests: testthat (≥ 3.0.0)
Published: 2021-10-04
Author: Siddhartha Kundu <2021: Manuscript Under Preparation>
Maintainer: Siddhartha Kundu <siddhartha_kundu at aiims.edu>
License: GPL-3
NeedsCompilation: no
CRAN checks: ReDirection results

Documentation:

Reference manual: ReDirection.pdf

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Package source: ReDirection_1.0.1.tar.gz
Windows binaries: r-devel: ReDirection_1.0.1.zip, r-release: ReDirection_1.0.1.zip, r-oldrel: ReDirection_1.0.1.zip
macOS binaries: r-release (arm64): ReDirection_1.0.1.tgz, r-oldrel (arm64): ReDirection_1.0.1.tgz, r-release (x86_64): ReDirection_1.0.1.tgz
Old sources: ReDirection archive

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