Description Details Objects from the Class Slots Extends Methods Note Author(s) References See Also Examples
The class sysBiolAlg_room
holds an object of class
optObj
which is generated to meet the
requirements of the ROOM algorithm.
The initialize
method has the following arguments:
An object of class modelorg
.
A numeric vector holding an optimal wild type flux distribution for the
given model. If missing, a default value is computed based on FBA.
If given, arguments solver
and method
are used to calculate
the dafault, but solverParm
is not.
A single numeric value giving the relative range of tolerance, see
Details below.
Default: 0.03
.
A single numeric value giving the absolute range of tolerance, see
Details below.
Default: 0.001
.
Boolean. If TRUE
, the problem object is formulated as linear
program. See Details below.
Default: FALSE
.
Boolean. If TRUE
, the problem object is formulated as linear
program. See Details below.
Default: FALSE
.
A single numerical value used as a maximum value for upper variable
and contraint bounds.
Default: SYBIL_SETTINGS("MAXIMUM")
.
A character vector giving the variable names. If set to NULL
,
the reaction id's of model
are used.
Default: NULL
.
A character vector giving the constraint names. If set to NULL
,
the metabolite id's of model
are used.
Default: NULL
.
A single character string containing a name for the problem object.
Default: NULL
.
Scaling options used to scale the constraint matrix. If set to
NULL
, no scaling will be performed
(see scaleProb
).
Default: NULL
.
A single character string containing a file name to which the problem
object will be written in LP file format.
Default: NULL
.
Further arguments passed to the initialize method of
sysBiolAlg
. They are solver
,
method
and solverParm
.
The problem object is built to be capable to perform the ROOM algorithm with a given model, which is basically the solution of a mixed integer programming problem
max sum (v_j,del  v_i,wt)^2 for i,j = 1, ..., n s.t. Sv = 0 a_i <= v_i <= b_i for i = 1, ..., n
with S being the stoichiometric matrix, a_i
and b_i being the lower and upper bounds for flux (variable)
i.
The total number of fluxes of the optimization problem is denoted by n.
Here, w is the optimal wild type flux distribution. This can be set via
the argument wtflux
. If wtflux
is NULL
(the default), the
wild type flux distribution will be calculated by a standard FBA.
All variables y_i are binary, with y_i = 1 for a significant flux
change in v_i and y_i = 0 otherwise. Thresholds determining the
significance of a flux change are given in w^u and w^l, with
delta and epsilon specifying absolute and
relative ranges in tolerance [Shlomi et al. 2005].
The Boolean argument LPvariant
relax the binary contraints to
0 <= y_i <= 1 so that the problem becomes a linear
program.
The optimization can be executed by using optimizeProb
.
Objects can be created by calls of the form
sysBiolAlg(model, algorithm = "room", ...)
.
Arguments to ...
which are passed to method initialize
of class
sysBiolAlg_room
are described in the Details section.
wu
:Object of class "numeric"
containing the upper threshold for a significant flux change,
see Details below.
wl
:Object of class "numeric"
containing the lower threshold for a significant flux change,
see Details below.
fnc
:Object of class "integer"
containing the number of reactions in the entire metabolic network
(argument model
to the constructor function
sysBiolAlg
).
fnr
:Object of class "integer"
containing the number of metabolites in the entire metabolic network
(argument model
to the constructor function
sysBiolAlg
).
problem
:Object of class "optObj"
containing the problem object.
algorithm
:Object of class "character"
containing the name of the algorithm.
nr
:Object of class "integer"
containing the number of rows of the problem object.
nc
:Object of class "integer"
containing the number of columns of the problem object
fldind
:Object of class "integer"
pointers to columns (variables) representing a flux (reaction) in the
original network. The variable fldind[i]
in the problem object
represents reaction i
in the original network.
alg_par
:Object of class "list"
containing a named list containing algorithm specific parameters.
Class "sysBiolAlg"
, directly.
signature(object = "sysBiolAlg_room")
:
runs optimization on the given problem object
(see optimizeProb
for details).
If using glpkAPI as MIP solver, consider to set parameter
PRESOLVE
to GLP_ON
.
Gabriel GeliusDietrich <geliudie@uniduesseldorf.de>
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Shlomi, T., Berkman, O. and Ruppin, E. (2005) Regulatory on/off minimization of metabolic flux changes after genetic pertubations. PNAS 102, 7695–7700.
Constructor function sysBiolAlg
and
superclass sysBiolAlg
.
1  showClass("sysBiolAlg_room")

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