blockedReact: Find Blocked Reactions in a Metabolic Network
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Details Value Author(s) See Also

A blocked Reaction in a metabolic network can not be used by the network, given the stiochiometric matrix of the network and a set of input and output fluxes.

  blockedReact(model,
               tol = SYBIL_SETTINGS("TOLERANCE"),
               exex = TRUE,
               fld = FALSE,
               retOptSol = FALSE,
               verboseMode = 2,
               ...)

`model`	An object of class `modelorg`.
`tol`	Tolerance value. Default: `SYBIL_SETTINGS("TOLERANCE")`.
`exex`	Boolean, if set to `TRUE`, exchange reactions found by `findExchReact` are excluded from the analysis. Default: `TRUE`.
`fld`	Boolean. Save the resulting flux distributions. Default: `FALSE`
`retOptSol`	Boolean. Return an object of class `optsol_blockedReact` or just a list containing the results. Default: `FALSE`.
`verboseMode`	An integer value indicating the amount of output to stdout: 0: nothing, 1: status messages, 2: like 1 plus a progress indicator. Default: `2`.
`...`	Further arguments passed to `sysBiolAlg`. Argument `solverParm` is a good candidate.

A reaction i is considered to be ‘blocked’, if its calculated reaction rate v[i] is -tol < v[i] < tol. Reaction rates are calculated via linear optimization: maximizing and minimizing each reaction rate. If the difference of the maximum and the minimum is not larger than tol, that particular reaction is blocked, given the current side conditions (exchange fluxes).

If argument retOptsol is set to TRUE, an object of class optsol_blockedReact is returned, otherwise a logical vector with length equal to the number of reactions of the network. If element i equals TRUE, reaction i is blocked.

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

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

modelorg, optsol_blockedReact and SYBIL_SETTINGS.

sybil documentation built on May 31, 2021, 5:08 p.m.