Package index • cobrar

Model import and export helpers

readSBMLmod(): Reads an SBML file and constructs an object of class 'ModelOrg'

readSybilmod(): Reads a sybil model file and constructs an object of cobrar's class 'ModelOrg'

writeSBMLmod(): Exports a Metabolic Network in SBML Format

Model manipulation tools

addCompartment(): Add compartments or update their data

addConstraint(): Add constraints to model

addGene(): Add genes or update their data

addMetabolite(): Add metabolites or update their data

addReact(): Add or modify a reaction

addSubsystem(): Add subsystems or update their data

changeBounds(): Change flux bounds

changeObjFunc(): Change the objective function

setObjDir(): Set objective direction

rmCompartment(): Remove compartments from a model

rmConstraint(): Remove constraints

rmGene(): Remove genes from a model

rmMetabolite(): Remove metabolites from a model

rmReact(): Remove reactions from a model

rmSubsystem(): Remove subsystems from a model

Model characteristics

checkCompartmentId(): Check compartment IDs and Indices

checkGeneId(): Check gene IDs and Indices

checkMetId(): Check metabolite IDs and Indices

checkReactId(): Check reaction IDs and Indices

checkSubsystemId(): Check subsystem IDs and Indices

comp_num(): Number of compartments

comp_pos(): Index of compartment(s)

constraint_num(): Number of constraints

met_num(): Number of metabolites

met_pos(): Index of metabolite(s)

gene_num(): Number of genes

gene_pos(): Index of gene(s)

geneDel(): Identify reactions affected by gene knockouts

deadEndMetabolites(): Identify dead end metabolites

findExchReact(): Find exchange reactions

printConstraint(): Print Constraint(s)

printReaction(): Print reaction(s)

react_num(): Number of reactions

react_pos(): Index of reaction(s)

show(<ModelOrg>): Print a short summary of a metabolic network model

subsys_num(): Number of subsystems

subsys_pos(): Index of subsystem(s)

guessBMReaction(): Guess biomass reaction(s)

Flux prediction algorithms

fba(): Flux Balance Analysis

fva(): Flux Variability Analysis (FVA)

pfba(): Parsimonious Flux Balance Analysis (pFBA)

pfbaHeuristic(): Heuristic parsimonious Flux Balance Analysis (pFBA)

Flux analysis tools

getExchanges(): Get metabolite exchange rates

show(<FluxPrediction>): Print a short summary of a flux prediction result

Community model functions

joinModels(): Join multiple metabolic models to form a community

fixBMRatios(): Fixate biomass ratios

fluxBMCoupling(): Couple reaction flux bounds to biomass production

Chemoinformatics

countElements(): Count elements in formulas

elements(): Data frame of elements and their average weights

mass(): Calculate molar mass of molecules

Object classes

Constraints-class Constraints: Structure of Constraints Class

FluxPrediction-class FluxPrediction: Structure of FluxPrediction Class

ModelOrg-class ModelOrg: Structure of ModelOrg Class

ModelComm-class ModelComm: Structure of ModelComm Class

Setup

COBRAR_SETTINGS(): Set and get central cobrar parameters

Internal LP solver connectors

addCols(): Add columns to LP problem

addRows(): Add rows to LP problem

addSingleConstraint(): Add single constraint

fvaJob(): Wrapper function for efficient FVA

getColsPrimal(): Retrieve column primal value

getObjValue(): Get the objective value of a solved LP problem

getRedCosts(): Retrieve column reduced costs

getSolStat(): Get the solver status

loadLPprob(): Initialize a LP problem

loadMatrix(): Populate a constraint-X-variable matrix

setColsBndsObjCoefs(): Set column bounds and objective coefficients

setColsKind(): Set column types

setObjDirection(): Set objective direction

setRowsBnds(): Set row bounds

solveLp(): Solve an LP problem

LPproblem-class LPproblem: Structure of LPproblem Class

LPproblem_glpk-class: Structure of LPproblem_glpk Class