## ----setup, echo=FALSE, results='hide', warning=FALSE, error=FALSE, message=FALSE, cache=FALSE---- library(knitr) opts_chunk$set( cache = FALSE, echo = TRUE, warning = FALSE, error = FALSE, message = FALSE ) ## ----------------------------------------------------------------------------- library(CARNIVAL) load(file = system.file("toy_perturbations_ex1.RData", package = "CARNIVAL")) load(file = system.file("toy_measurements_ex1.RData", package = "CARNIVAL")) load(file = system.file("toy_network_ex1.RData", package = "CARNIVAL")) carnivalOptions <- defaultLpSolveCarnivalOptions() # Output dir dir.create("ToyExample1", showWarnings = FALSE) carnivalOptions$outputFolder <- "ToyExample1" # lpSolve resultsLpSolve <- runVanillaCarnival( perturbations = toy_perturbations_ex1, measurements = toy_measurements_ex1, priorKnowledgeNetwork = toy_network_ex1, carnivalOptions = carnivalOptions) ## ----------------------------------------------------------------------------- print(resultsLpSolve) ## ----------------------------------------------------------------------------- saveRDS(resultsLpSolve, "ToyExample1/network_solution.Rds") ## ----------------------------------------------------------------------------- load(file = system.file("toy_measurements_ex2.RData", package="CARNIVAL")) load(file = system.file("toy_network_ex2.RData", package="CARNIVAL")) carnivalOptions <- defaultLpSolveCarnivalOptions() # Output dir dir.create("ToyExample2", showWarnings = FALSE) carnivalOptions$outputFolder <- "ToyExample2" # lpSolve toy_network_ex2 <- as.data.frame(toy_network_ex2) colnames(toy_network_ex2) <- c("source", "interaction", "target") toy_measurements_ex2 <- c("M1" = 1, "M2" = 1, "M3" = 1) inverseCarnivalResults <- runInverseCarnival( measurements = c(toy_measurements_ex2), priorKnowledgeNetwork = toy_network_ex2, carnivalOptions = carnivalOptions) ## ----------------------------------------------------------------------------- print(inverseCarnivalResults) ## ----------------------------------------------------------------------------- load(file = system.file("toy_perturbations_ex1.RData", package = "CARNIVAL")) load(file = system.file("toy_measurements_ex1.RData", package = "CARNIVAL")) load(file = system.file("toy_network_ex1.RData", package = "CARNIVAL")) carnivalOptions <- defaultLpSolveCarnivalOptions() # Output dir dir.create("ToyExample3", showWarnings = FALSE) carnivalOptions$outputFolder <- "ToyExample3" # lpSolve generateLpFileCarnival(perturbations = toy_perturbations_ex1, measurements = toy_measurements_ex1, priorKnowledgeNetwork = toy_network_ex1, carnivalOptions = carnivalOptions) ## ----------------------------------------------------------------------------- lpFilename <- "toy_files_vignettes/lpFile_t18_01_53d28_04_2021n4.lp" parsedDataFile <- "toy_files_vignettes/parsedData_t18_01_53d28_04_2021n4.RData" resultsFromLp <- runFromLpCarnival(lpFile = lpFilename, parsedDataFile = parsedDataFile, carnivalOptions = defaultLpSolveCarnivalOptions()) ## ----------------------------------------------------------------------------- resultsFromLp ## ----------------------------------------------------------------------------- sessionInfo()