generateLpFileCarnival
generateLpFileCarnival( perturbations = NULL, measurements, priorKnowledgeNetwork, weights = NULL, carnivalOptions = defaultLpSolveCarnivalOptions() )
perturbations | (optional, if inverse CARNIVAL flavour is used further) vector of targets of perturbations. |
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measurements | vector of the measurements (i.e. DoRothEA/VIPER normalised enrichment scores) |
priorKnowledgeNetwork | data frame of the prior knowledge network |
weights | (optional) vector of the additional weights: e.g. PROGENy pathway scores or measured protein activities. |
carnivalOptions | the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultCplexCarnivalOptions, defaultCbcCarnivalOptions. |
paths to .lp file and .RData file that can be used for runFromLpCarnival()
Prepares the input data for the run: tranforms data into lp file and .Rdata file. These files can be reused to run CARNIVAL without preprocessing step using runCarnivalFromLp(..)
load(file = system.file("toy_perturbations_ex1.RData", package="CARNIVAL")) load(file = system.file("toy_measurements_ex1.RData", package="CARNIVAL")) load(file = system.file("toy_network_ex1.RData", package="CARNIVAL")) ## lpSolve res1 = generateLpFileCarnival(perturbations = toy_perturbations_ex1, measurements = toy_measurements_ex1, priorKnowledgeNetwork = toy_network_ex1, carnivalOptions = defaultLpSolveCarnivalOptions())#>#>#>#>#>#>#>#>#>#>#>#>#>#> #>res1["lpFile"] ##path to generated lp file#> lpFile #> "/Users/olgaivanova/GoogleDrive/_PhD_Heidelberg/playground/carnival_style/carnival/docs/reference/lpFile_t01_55_44d12_05_2021n45.lp"res1["parsedDataFile"] ##path to data file used during generation#> parsedDataFile #> "/Users/olgaivanova/GoogleDrive/_PhD_Heidelberg/playground/carnival_style/carnival/docs/reference/parsedData_t01_55_44d12_05_2021n45.RData"## Examples for cbc and cplex are commented out because these solvers are not part of R environment ## and need to be installed separately ## ## cbc ## res2 = generateLpFileCarnival(perturbations = toy_perturbations_ex1, ## measurements = toy_measurements_ex1, ## priorKnowledgeNetwork = toy_network_ex1, ## carnivalOptions = defaultCbcCarnivalOptions()) ## ## res2["lpFile"] ##path to generated lp file ## res2["parsedDataFile"] ##path to data file used during generation ## ## cplex ## res3 = generateLpFileCarnival(perturbations = toy_perturbations_ex1, ## measurements = toy_measurements_ex1, ## priorKnowledgeNetwork = toy_network_ex1, ## carnivalOptions = defaultCplexCarnivalOptions()) ## ## res3["lpFile"] ##path to generated lp file ## res3["parsedDataFile"] ##path to data file used during generation