sybil (version 2.0.0)

summaryOptsol-class: Class "summaryOptsol"

Description

Class summaryOptsol stores a summary of instances of class '>optsol.

Objects from the Class

Objects can be created by calls of the form summaryOptsol(opt, mod).

Slots

mod_id:

Object of class "character" containing the model id of the analyzed model.

mod_key:

Object of class "character" containing the model key of the used model.

nzeros:

Object of class "integer" giving the number of zeros in the flux distribution.

nnonzero:

Object of class "integer" giving the number of non-zeros in the flux distribution.

mod_obj:

Object of class "numeric" containing the objective coefficients of the model.

ex_met:

Object of class "character" containing the id's of exchange metabolites. These are metabolites which are transported across the system boundary.

ex_val:

Object of class "Matrix" with each column being the flux distribution of the exchange metabolites of one optimization.

react_id:

Object of class "list" with each list element containing a set of reaction id's limiting one optimization. A reactions is considered as “limiting”, if it has a non-zero flux value and if its flux value hits an upper or lower bound.

chksol:

Object of class "checksol" describing return values of the mathematical programming software and solution status.

Methods

ex_met

signature(object = "summaryOptsol"): gets the ex_met slot.

ex_val

signature(object = "summaryOptsol"): gets the ex_val slot.

plot:

signature(x = "summaryOptsol"): plots a histogram of the values of the objective function in optimal state. Additional arguments can be passed to histogram via the … argument.

image

signature(x = "summaryOptsol"): plots a grey-scale representation of the exchange fluxes of the flux distribution. Black: metabolite is produced, grey: metabolite is imported. Further arguments are:

printOut

A single logical value. If set to FALSE, a trellis.object is returned invisibly. Otherwise, a plot is drawn additionally. Default: TRUE.

...

Further arguments to image-methods.

mod_id

signature(object = "summaryOptsol"): gets the mod_id slot.

mod_id<-

signature(object = "summaryOptsol"): sets the mod_id slot.

mod_key

signature(object = "summaryOptsol"): gets the mod_key slot.

mod_key<-

signature(object = "summaryOptsol"): sets the mod_key slot.

mod_obj

signature(object = "summaryOptsol"): gets the mod_obj slot.

mod_obj<-

signature(object = "summaryOptsol"): sets the mod_obj slot.

nnzero

signature(object = "summaryOptsol"): gets the nnonzero slot.

nzeros

signature(object = "summaryOptsol"): gets the nzeros slot.

printExchange

signature(object = "summaryOptsol"): prints a matrix indicating wether a particular metabolite is taken up or produced by the metabolic network given certain conditions. Each line corresponds to one metabolite and each column to one optimization. A "-" indicates uptake and "+" indicates excretion. A whitespace character " " is used, if the metabolite is unused. Further arguments are:

i

A numeric vector indicating the metabolites (rows) to print: i[x] points to matabolite ec_met(object)[x].

j

A numeric vector indicating the optimizations (columns) to print.

dense

A single Boolean value. If set to TRUE, each column has a column with of one letter.

See Also

Constructor function summaryOptsol, class '>optsol and class '>modelorg.

Examples

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