sybil (version 2.2.0)

optsol_fluxVar-class: Class "optsol_fluxVar"

Description

Structure of the class "optsol_fluxVar". Objects of that class are returned by the function fluxVar.

Objects from the Class

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

Slots

react:

Object of class "reactId" containing reaction id's for which ranges were calculated.

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.

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:

signature(object = "optsol_fluxVar"): gets the react slot.

react<-:

signature(object = "optsol_fluxVar"): sets the react slot.

maxSol:

signature(object = "optsol_fluxVar")(slot): returns the values in the slot given in slot for optimizations in “max” direction.

minSol:

signature(object = "optsol_fluxVar")(slot): returns the values in the slot given in slot for optimizations in “min” direction.

plot

signature(x = "optsol_fluxVar", y = "missing") (ylim, xlab = "", ylab = "Value", pch = 20, col = "black", collower, colupper, pchupper, pchlower, dottedline = FALSE, baseline = 0, ...): plots the range of values each flux can have still giving an optimal objective function value.

ylim

scaling of y-axis, if missing, the maximum and minimum value of all optimizations is used (rounded to the next smaller/larger integer value).

xlab

label of x-axis, see also par.

ylab

label of y-axis, see also par.

pch

how to plot the points, see also par.

col

color of the plot, see also par.

collower

color of the minimum range value. Default col.

colupper

color of the maximum range value. Default col.

pchupper

how to plot the point for the maximum range value. Default pch.

pchlower

how to plot the point for the minimum range value. Default pch.

dottedline

if set to FALSE, from each minimum range value a dotted line to the corresponding x-axis label will be plotted. Default FALSE.

baseline

plot a horizontal dashed line at the value of baseline. Default 0. If set to NA, no baseline will be plotted.

connect

if set to TRUE, a solid connecting line will be drawn between the minimum and maximum value of one reaction. Default TRUE.

colconnect

color of the connecting line. Default "black".

…

further arguments to the plot function.

plotRangeVar

signature(object = "optsol_fluxVar") (...): plot a histogram of the span of the minimum and maximum range values for each flux.

...

further arguments to the hist function.

blReact

signature(object = "optsol_fluxVar") (tol = SYBIL_SETTINGS("TOLERANCE")): returns a logical vector of length equal to the number of reactions analyzed during flux variance analysis (number of optimizations divided by two). If blReact(object)[j] equals TRUE, reaction j is considered to be blocked (zero flux rate) given the used conditions. A reaction \(j\) is considered to be ‘blocked’, if its calculated range of reaction rates does not exceed 0 +/- tol.

tol

limit of tolerance.

See Also

checkOptSol and '>optsol

Examples

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