optsol_fluxVar-class: Class '"optsol_fluxVar"'
In sybil: Efficient Constrained Based Modelling

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

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

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

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.

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

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.