modelorg-class: Structure of Class "modelorg"

In sybil: Efficient Constrained Based Modelling

Description

Structure of the class "modelorg". Objects of that class are returned by functions like readTSVmod.

Structure of the class "react". This depicts a subset of a metabolic model that contains only one reaction. Multiple react objects can be combined to an "modelorg" object.

Objects from the Class

Objects can be created by calls of the function modelorg:

test <- modelorg(id = "foo", name = "bar", subSys = NULL, compartment = NULL).

id:

a single character string giving the model id.

name:

a single character string giving the model name.

subSys:

an optional single character string giving the metabolic subsystems of the model. Default: NULL

compartment:

an optional single character string giving the compartments of the model. Default: NULL

This constructor also generates the model key used in slot mod_key.

Slots

mod_desc:

Object of class "character" containing a description of the model.

mod_name:

Object of class "character" indicating the model name.

version:

Object of class "character" indicating the model version.

mod_id:

Object of class "character" indicating the model id.

mod_key:

Object of class "character" containing a single character string functioning as a unique key to a model object.

mod_attr:

Object of class "data.frame" to store additional attributes of the model.

mod_compart:

Object of class "character" containing the model compartments.

comp_attr:

Object of class "data.frame" to store additional attributes for each compartment.

met_num:

Object of class "integer" indicating the number of metabolites.

met_id:

Object of class "character" containing the metabolite id's.

met_name:

Object of class "character" containing the metabolite names.

met_comp:

Object of class "integer" containing the metabolites compartment.

met_attr:

Object of class "data.frame" to store additional attributes for each metabolite.

met_single:

Object of class "logical" with length met_num. Element i is TRUE, if metabolite i appears only once in S.

met_de:

Object of class "logical" with length met_num. Element i is TRUE, if metabolite i is a dead end metabolite.

react_num:

Object of class "integer" indicating the number of reactions.

react_rev:

Object of class "logical" indicating whether a reaction is reversible or not.

react_id:

Object of class "character" containing the reaction id's.

react_name:

Object of class "character" containing the reaction names.

react_attr:

Object of class "data.frame" to store additional attributes for each reaction.

react_single:

Object of class "logical" with length react_num. Element i is TRUE, if reaction i uses metabolites appearing only once in S.

react_de:

Object of class "logical" with length react_num. Element i is TRUE, if reaction i uses dead end metabolites.

S:

Object of class "matrix" containing the stoichiometric matrix.

lowbnd:

Object of class "numeric" containing the reactions lower bounds.

uppbnd:

Object of class "numeric" containing the reactions upper bounds.

obj_coef:

Object of class "numeric" containing the objective coefficients.

gprRules:

Object of class "character" containing the gene-reaction association rules in computable form.

genes:

Object of class "list" containing the genes corresponding to each reaction. Every list element is a vector of the type character.

gpr:

Object of class "character" containing the gene-reaction association rules for each reaction.

allGenes:

Object of class "character" containing a unique list of all genes.

rxnGeneMat:

Object of class "matrix" containing a reaction to gene mapping.

subSys:

Object of class "matrix" giving one or more subsystem name for each reaction.

Methods

allGenes<-:

signature(object = "modelorg"): sets the allGenes slot.

allGenes:

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

dim:

signature(object = "modelorg"): gets the dimension attribute of slot S.

genes<-:

signature(object = "modelorg"): sets the genes slot.

genes:

signature(object = "modelorg"): gets the genes slot.

gpr<-:

signature(object = "modelorg"): sets the gpr slot.

gpr:

signature(object = "modelorg"): gets the gpr slot.

gprRules<-:

signature(object = "modelorg"): sets the gprRules slot.

gprRules:

signature(object = "modelorg"): gets the gprRules slot.

lowbnd<-:

signature(object = "modelorg"): sets the lowbnd slot.

lowbnd:

signature(object = "modelorg"): gets the lowbnd slot.

met_comp<-:

signature(object = "modelorg"): sets the met_comp slot.

met_comp:

signature(object = "modelorg"): gets the met_comp slot.

met_de<-:

signature(object = "modelorg"): sets the met_de slot.

met_de:

signature(object = "modelorg"): gets the met_de slot.

met_id<-:

signature(object = "modelorg"): sets the met_id slot.

met_id:

signature(object = "modelorg"): gets the met_id slot.

met_name<-:

signature(object = "modelorg"): sets the met_name slot.

met_name:

signature(object = "modelorg"): gets the met_name slot.

met_num<-:

signature(object = "modelorg"): sets the met_num slot.

met_num:

signature(object = "modelorg"): gets the met_num slot.

met_single<-:

signature(object = "modelorg"): sets the met_single slot.

met_single:

signature(object = "modelorg"): gets the met_single slot.

mod_compart<-:

signature(object = "modelorg"): sets the mod_compart slot.

mod_compart:

signature(object = "modelorg"): gets the mod_compart slot.

mod_desc<-:

signature(object = "modelorg"): sets the mod_desc slot.

mod_desc:

signature(object = "modelorg"): gets the mod_desc slot.

mod_id<-:

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

mod_id:

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

mod_key<-:

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

mod_key:

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

mod_name<-:

signature(object = "modelorg"): sets the mod_name slot.

mod_name:

signature(object = "modelorg"): gets the mod_name slot.

obj_coef<-:

signature(object = "modelorg"): sets the obj_coef slot.

obj_coef:

signature(object = "modelorg"): gets the obj_coef slot.

printObjFunc:

signature(object = "modelorg"): prints the objective function in a human readable way.

react_de<-:

signature(object = "modelorg"): sets the react_de slot.

react_de:

signature(object = "modelorg"): gets the react_de slot.

react_id<-:

signature(object = "modelorg"): sets the react_id slot.

react_id:

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

react_name<-:

signature(object = "modelorg"): sets the react_name slot.

react_name:

signature(object = "modelorg"): gets the react_name slot.

react_num<-:

signature(object = "modelorg"): sets the react_num slot.

react_num:

signature(object = "modelorg"): gets the react_num slot.

react_rev<-:

signature(object = "modelorg"): sets the react_rev slot.

react_rev:

signature(object = "modelorg"): gets the react_rev slot.

react_single<-:

signature(object = "modelorg"): sets the react_single slot.

react_single:

signature(object = "modelorg"): gets the react_single slot.

rxnGeneMat<-:

signature(object = "modelorg"): sets the rxnGeneMat slot.

rxnGeneMat:

signature(object = "modelorg"): gets the rxnGeneMat slot.

show:

signature(object = "modelorg"): prints some details specific to the instance of class modelorg.

Snnz:

signature(object = "modelorg"): prints the number of non-zero elements in S.

S<-:

signature(object = "modelorg"): sets the S slot as matrix, see Details below.

S:

signature(object = "modelorg"): gets the S slot as matrix.

subSys<-:

signature(object = "modelorg"): sets the subSys slot.

subSys:

signature(object = "modelorg"): gets the subSys slot.

uppbnd<-:

signature(object = "modelorg"): sets the uppnds slot.

uppbnd:

signature(object = "modelorg"): gets the uppbnd slot.

version<-:

signature(object = "modelorg"): sets the version slot.

version:

signature(object = "modelorg"): gets the version slot.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

modelorg_irrev for models in irreversible format.

Examples

  showClass("modelorg")

  ## print human readable version of the objective function
  data(Ec_core)
  printObjFunc(Ec_core)

  ## change objective function and print
  Ec_objf <- changeObjFunc(Ec_core, c("EX_etoh(e)", "ETOHt2r"), c(1, 2))
  printObjFunc(Ec_objf)

sybil documentation built on May 31, 2021, 5:08 p.m.