sybil (version 2.0.0)

optsol_fluxdel-class: Class "optsol_fluxdel"

Description

Structure of the class "optsol_fluxdel". Objects of that class are returned by the function oneFluxDel.

Objects from the Class

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

Slots

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 reaction id's of constrained reactions. Each row of the matrix represents one set of simultaneously constrained reactions.

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_optimizeProb", directly. Class "'>optsol", by class "optsol_optimizeProb", distance 2.

Methods

react_id:

signature(object = "optsol_fluxdel"): gets the react_id slot.

react_id<-:

signature(object = "optsol_fluxdel") sets the react_id slot.

allGenes:

signature(object = "optsol_fluxdel"): gets the allGenes slot.

allGenes<-:

signature(object = "optsol_fluxdel") sets the allGenes slot.

chlb:

signature(object = "optsol_fluxdel"): gets the chlb slot.

chlb<-:

signature(object = "optsol_fluxdel") sets the chlb slot.

chub:

signature(object = "optsol_fluxdel"): gets the chub slot.

chub<-:

signature(object = "optsol_fluxdel"): sets the chub slot.

dels:

signature(object = "optsol_fluxdel"): gets the dels slot.

dels<-:

signature(object = "optsol_fluxdel") sets the dels slot.

algorithm:

signature(object = "optsol_fluxdel"): gets the algorithm slot.

algorithm<-:

signature(object = "optsol_fluxdel") sets the algorithm slot.

% \item{\code{ind2id}:}{ % \code{signature(object = "optsol_fluxdel")}(\code{slotN}): translates the % indices in \code{slotN} into corresponding gene or reaction id's. Possible % values for \code{slotN} are: \code{"dels"}. % }

lethal:

signature(object = "optsol_fluxdel")(wt, tol): returns a logical vector of length num_of_prob(object). Argument wt is an optimal (wild type) growth rate, e.g. computed via FBA. If the absolute growth ratio (mod_obj(object)/wt) of knock-out i is less than tol, the deletion is considered as lethal. If lethal(object)[i] is TRUE, deletion [i] is lethal.

deleted:

signature(object = "optsol_fluxdel")(i): gets the ith element of the dels slot.

[:

signature(x = "optsol_fluxdel"): access like a vector. x[i] returns a new object of class optsol_fluxdel containing the ith deletion experiment.

See Also

checkOptSol, '>optsol, '>optsol_genedel and '>optsol_optimizeProb

Examples

# NOT RUN {
  showClass("optsol_fluxdel")
# }