Constraint-Based Metabolic Network Analysis in R

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Documentation for package ‘cobrar’ version 0.2.3

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A C D E F G J L M P R S W

-- A --

addCols Add columns to LP problem
addCols,LPproblem_glpk Add columns to LP problem
addCols-method Add columns to LP problem
addCompartment Add compartments or update their data
addConstraint Add constraints to model
addConstraint,ModelOrg,character,numeric,character Add constraints to model
addConstraint,ModelOrg,list,list,character Add constraints to model
addConstraint-method Add constraints to model
addGene Add genes or update their data
addMetabolite Add metabolites or update their data
addReact Add or modify a reaction
addRows Add rows to LP problem
addRows,LPproblem_glpk Add rows to LP problem
addRows-method Add rows to LP problem
addSingleConstraint Add single constraint
addSingleConstraint,LPproblem_glpk Add single constraint
addSingleConstraint-method Add single constraint
addSubsystem Add subsystems or update their data

-- C --

changeBounds Change flux bounds
changeObjFunc Change the objective function
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
COBRAR_SETTINGS Set and get central cobrar parameters
comp_num Number of compartments
comp_num,ModelOrg Number of compartments
comp_num-method Number of compartments
comp_pos Index of compartment(s)
comp_pos,ModelOrg,character Index of compartment(s)
comp_pos,ModelOrg,logical Index of compartment(s)
comp_pos,ModelOrg,missing Index of compartment(s)
comp_pos,ModelOrg,numeric Index of compartment(s)
comp_pos-method Index of compartment(s)
Constraints Structure of Constraints Class
Constraints-class Structure of Constraints Class
constraint_num Number of constraints
constraint_num,ModelOrg Number of constraints
constraint_num-method Number of constraints
countElements Count elements in formulas

-- D --

deadEndMetabolites Identify dead end metabolites
deleteLP Delete an LP problem
deleteLP,LPproblem_glpk Delete an LP problem
deleteLP-method Delete an LP problem

-- E --

elements Data frame of elements and their average weights

-- F --

fba Flux Balance Analysis
findExchReact Find exchange reactions
findExchReact,ModelComm Find exchange reactions
findExchReact,ModelOrg Find exchange reactions
findExchReact-method Find exchange reactions
fixBMRatios Fixate biomass ratios
fluxBMCoupling Couple reaction flux bounds to biomass production
FluxPrediction Structure of FluxPrediction Class
FluxPrediction-class Structure of FluxPrediction Class
frog FROG: Reproducible fitness and robustness diagnostics for constraint-based models
frog,character FROG: Reproducible fitness and robustness diagnostics for constraint-based models
frog,ModelOrg FROG: Reproducible fitness and robustness diagnostics for constraint-based models
frog-method FROG: Reproducible fitness and robustness diagnostics for constraint-based models
fva Flux Variability Analysis (FVA)
fvaJob Wrapper function for efficient FVA
fvaJob,LPproblem_glpk Wrapper function for efficient FVA
fvaJob-method Wrapper function for efficient FVA

-- G --

geneDel Identify reactions affected by gene knockouts
gene_num Number of genes
gene_num,ModelOrg Number of genes
gene_num-method Number of genes
gene_pos Index of gene(s)
gene_pos,ModelOrg,character Index of gene(s)
gene_pos,ModelOrg,missing Index of gene(s)
gene_pos,ModelOrg,numeric Index of gene(s)
gene_pos-method Index of gene(s)
getColsPrimal Retrieve column primal value
getColsPrimal,LPproblem_glpk Retrieve column primal value
getColsPrimal-method Retrieve column primal value
getExchanges Get metabolite exchange rates
getObjValue Get the objective value of a solved LP problem
getObjValue,LPproblem_glpk Get the objective value of a solved LP problem
getObjValue-method Get the objective value of a solved LP problem
getRedCosts Retrieve column reduced costs
getRedCosts,LPproblem_glpk Retrieve column reduced costs
getRedCosts-method Retrieve column reduced costs
getSolStat Get the solver status
getSolStat,LPproblem_glpk Get the solver status
getSolStat-method Get the solver status
guessBMReaction Guess biomass reaction(s)
guessBMReaction,ModelComm Guess biomass reaction(s)
guessBMReaction,ModelOrg Guess biomass reaction(s)
guessBMReaction-method Guess biomass reaction(s)

-- J --

joinModels Join multiple metabolic models to form a community

-- L --

loadLPprob Initialize a LP problem
loadLPprob,LPproblem_glpk Initialize a LP problem
loadLPprob-method Initialize a LP problem
loadMatrix Populate a constraint-X-variable matrix
loadMatrix,LPproblem_glpk Populate a constraint-X-variable matrix
loadMatrix-method Populate a constraint-X-variable matrix
LPproblem Structure of LPproblem Class
LPproblem-class Structure of LPproblem Class
LPproblem_glpk-class Structure of LPproblem_glpk Class

-- M --

mass Calculate molar mass of molecules
met_num Number of metabolites
met_num,ModelOrg Number of metabolites
met_num-method Number of metabolites
met_pos Index of metabolite(s)
met_pos,ModelOrg,character Index of metabolite(s)
met_pos,ModelOrg,missing Index of metabolite(s)
met_pos,ModelOrg,numeric Index of metabolite(s)
met_pos-method Index of metabolite(s)
ModelComm Structure of ModelComm Class
ModelComm-class Structure of ModelComm Class
ModelOrg Structure of ModelOrg Class
ModelOrg-class Structure of ModelOrg Class

-- P --

pfba Parsimonious Flux Balance Analysis (pFBA)
pfbaHeuristic Heuristic parsimonious Flux Balance Analysis (pFBA)
printConstraint Print Constraint(s)
printReaction Print reaction(s)

-- R --

react_num Number of reactions
react_num,ModelOrg Number of reactions
react_num-method Number of reactions
react_pos Index of reaction(s)
react_pos,ModelOrg,character Index of reaction(s)
react_pos,ModelOrg,missing Index of reaction(s)
react_pos,ModelOrg,numeric Index of reaction(s)
react_pos-method Index of reaction(s)
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'
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

-- S --

setColsBndsObjCoefs Set column bounds and objective coefficients
setColsBndsObjCoefs,LPproblem_glpk Set column bounds and objective coefficients
setColsBndsObjCoefs-method Set column bounds and objective coefficients
setColsKind Set column types
setColsKind,LPproblem_glpk Set column types
setColsKind-method Set column types
setObjDir Set objective direction
setObjDirection Set objective direction
setObjDirection,LPproblem_glpk Set objective direction
setObjDirection-method Set objective direction
setRowsBnds Set row bounds
setRowsBnds,LPproblem_glpk Set row bounds
setRowsBnds-method Set row bounds
show-method Print a short summary of a flux prediction result
show-method Print a short summary of a metabolic network model
solveLp Solve an LP problem
solveLp,LPproblem_glpk Solve an LP problem
solveLp-method Solve an LP problem
subsys_num Number of subsystems
subsys_num,ModelOrg Number of subsystems
subsys_num-method Number of subsystems
subsys_pos Index of subsystem(s)
subsys_pos,ModelOrg,character Index of subsystem(s)
subsys_pos,ModelOrg,logical Index of subsystem(s)
subsys_pos,ModelOrg,missing Index of subsystem(s)
subsys_pos,ModelOrg,numeric Index of subsystem(s)
subsys_pos-method Index of subsystem(s)

-- W --

writeSBMLmod Exports a Metabolic Network in SBML Format