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 preprocessing.
See also optimizeProb
.
postProc
:Object of class "ppProc"
containing the results of postprocessing.
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 yaxis, if missing, the maximum and minimum value of all optimizations is used (rounded to the next smaller/larger integer value).
xlab
label of xaxis, see also par
.
ylab
label of yaxis, 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 xaxis 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.
Gabriel GeliusDietrich <geliudie@uniduesseldorf.de>
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
checkOptSol
and optsol
1  showClass("optsol_fluxVar")

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