Man pages for saezlab/CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

addPerturbationNodesIntroduces a perturbation node connecting periphery nodes...
checkCarnivalOptionsChecks options provided for CARNIVAL
checkDataChecks the input data for correctness.
checkOptionsValidityChecks if provided option names are valid.
checkPriorKnowledgeNetworkChecks prior knowledge network for correct format.
createInternalDataRepresentationCreates internal data representation - variables for ILP...
defaultCbcSolveCarnivalOptionsSets default CARNIVAL options for cbc.
defaultCplexCarnivalOptionsSets default CARNIVAL options for cplex.
defaultCplexSpecificOptionsSets default options from cplex documentation.
defaultLpSolveCarnivalOptionsSets default CARNIVAL options for lpSolve.
generateLpFileCarnival'generateLpFileCarnival'
getOptionsListReturns the list of options needed/supported for each solver.
getSupportedSolversReturns the list of supported solvers.
getSupportedSolversFunctionsSupported solvers functions to work with all solvers in a...
isInputValidCarnivalChecks validity of all inputs of CARNIVAL
parseCplexLogParses the cplex log file and reads some basic information.
prepareForCarnivalRunPrepares ILP formulation and writes it to .lp file....
preprocessPriorKnowledgeNetworkPreprocesses prior knowledge network: correct nodes...
processSolutionExports the solution matrix to the final solution.
readOptionsReads options from json file.
runCARNIVAL'runCARNIVAL'
runFromLpCarnival'runCarnivalFromLp'
runInverseCarnival'runInverseCarnival'
runVanillaCarnival'runVanillaCarnival'
sendTaskToSolverExecutes the solve on the provided ILP formulation (in .lp...
setCarnivalOptionsSets CARNIVAL options for the solver.
solveCarnivalMain CARNIVAL function to execute the full pipeline: 1)...
solveCarnivalFromLpSends the ILP formulation defined in .lp file to solver. Uses...
solveWithCbcExecutes cbc solver on provided .lp file.
suggestedCbcSpecificOptionsSuggests cbc specific options.
suggestedCplexSpecificOptionsSuggests cplex specific options.s
writeParsedDataSaves all provided data together with generated variables for...
saezlab/CARNIVAL documentation built on May 13, 2021, 3:07 a.m.