optsol_genedel-class: Class '"optsol_genedel"'

In sybil: Efficient Constrained Based Modelling

Description

Structure of the class "optsol_genedel". Objects of that class are returned by the function geneDel.

Objects from the Class

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

Slots

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.

Extends

Class "optsol_fluxdel", directly. Class "optsol_optimizeProb", by class "optsol_fluxdel", distance 2. Class "optsol", by class "optsol_fluxdel", distance 3.

Methods

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 ith element of the dels slot.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

checkOptSol, optsol, optsol_fluxdel and optsol_optimizeProb

Examples

  showClass("optsol_genedel")

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