sybil (version 1.0.2)

blockedReact: Find Blocked Reactions in a Metabolic Network

Description

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.

Usage

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

Arguments

model

An object of class modelorg.

solver

Single character value. The solver to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").

method

Single character value. The optimization algorithm to use. Possible values depend on the setting in solver. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTIN

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 prepProbObj. Argument solverParm is a good candidate.

Value

• 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.

Details

A reaction $i$ is considered to be blocked, if its calculated reaction rate $v_i$ is $-\mathrm{tol} < v_i < \mathrm{tol}$. 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).

See Also

modelorg, optsol_blockedReact and SYBIL_SETTINGS.