Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

Structure of the class `"optsol_genedel"`

. Objects of that class are
returned by the function `geneDel`

.

Objects can be created by calls of the form
`new("optsol_genedel", ...)`

.

`fluxdels`

:-
Object of class

`"list"`

containing the reaction id's of constrained reactions (fluxes).`fluxdels(optsol_genedel)[[i]][j] = l`

: The deletion of gene`i`

requires the deletion of a set of fluxes`1..k`

(j*≤*k),`j`

being the j'th reaction of that set. `hasEffect`

:-
Object of class

`"logical"`

indicating whether deletion of gene`i`

has an effect or not. This is determined on basis of the`gprRules`

and not by optimizations. `chlb`

:Object of class

`"numeric"`

containing the new (changed) values for the columns lower bounds.`chub`

:Object of class

`"numeric"`

containing the new (changed) values for the columns upper bounds.`dels`

:-
Object of class

`"matrix"`

containing the gene id of constrained genes. Each row of the matrix represents one set of simultaneously constrained genes. `preProc`

:Object of class

`"ppProc"`

containing the results of pre-processing. See also`optimizeProb`

.`postProc`

:Object of class

`"ppProc"`

containing the results of post-processing. See also`optimizeProb`

.`mod_id`

:Object of class

`"character"`

containing the model id of the used model.`mod_key`

:Object of class

`"character"`

containing the model key of the used model.`solver`

:Object of class

`"character"`

indicating the used solver.`method`

:Object of class

`"character"`

indicating the used method.`algorithm`

:Object of class

`"character"`

containing the name of the algorithm used for optimizations.`num_of_prob`

:Object of class

`"integer"`

indicating the number of optimization problems.`lp_num_cols`

:Object of class

`"integer"`

indicating the number of columns.`lp_num_rows`

:Object of class

`"integer"`

indicating the number of rows.`lp_obj`

:Object of class

`"numeric"`

containing the optimal values of the objective function after optimization. If no flux distribution is available, slot`lp_obj`

contains the cross-product of the objective coefficients in slot`obj_coef`

and the part of the flux distribution in slot`fluxdist`

containing the values representing fluxes in the entire metabolic network (slot`fldind`

).`lp_ok`

:Object of class

`"integer"`

containing the exit code of the optimization.`lp_stat`

:Object of class

`"integer"`

containing the solution status of the optimization.`lp_dir`

:Object of class

`"character"`

indicating the direction of optimization.`obj_coef`

:Object of class

`"numeric"`

containing the objective coefficients of the used model (slot`obj_coef`

of an object of class`modelorg`

). These are not necessarily the objective coefficients of the used algorithm.`obj_func`

:Object of class

`"character"`

containing the objective function of the used model. Usually, it contains the return value of`printObjFunc`

.`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.`fluxdist`

:Object of class

`"fluxDistribution"`

containing the solutions flux distributions.`alg_par`

:Object of class

`"list"`

containing a named list containing algorithm specific parameters.

Class `"optsol_fluxdel"`

, directly.
Class `"optsol_optimizeProb"`

,
by class "optsol_fluxdel", distance 2.
Class `"optsol"`

, by class "optsol_fluxdel", distance 3.

`fluxdels`

:-
`signature(object = "optsol_genedel")`

: gets the`fluxdels`

slot. `fluxdels<-`

:-
`signature(object = "optsol_genedel")`

sets the`fluxdels`

slot. `hasEffect`

:-
`signature(object = "optsol_genedel")`

: gets the`hasEffect`

slot. `hasEffect<-`

:-
`signature(object = "optsol_genedel")`

: sets the`hasEffect`

slot.

`deleted`

:-
`signature(object = "optsol_genedel")`

(`i`

): gets the`i`

th element of the`dels`

slot.

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

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

`checkOptSol`

,
`optsol`

,
`optsol_fluxdel`

and
`optsol_optimizeProb`

1 | ```
showClass("optsol_genedel")
``` |

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