## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, fig.width = 7, fig.height = 5) ## ----getPackage, eval=FALSE------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("sRACIPE") ## ---- eval = FALSE--------------------------------------------------------- # BiocManager::install(“vivekkohar/sRACIPE”) ## ----Load, message=FALSE--------------------------------------------------- library(sRACIPE) ## ----eval=TRUE------------------------------------------------------------- library(sRACIPE) # Load a demo circuit data("demoCircuit") demoCircuit ## -------------------------------------------------------------------------- rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20, plots = FALSE, integrateStepSize = 0.1, simulationTime = 30) ## ----eval=TRUE------------------------------------------------------------- rSet <- sRACIPE::sracipeNormalize(rSet) rSet <- sRACIPE::sracipePlotData(rSet, plotToFile = FALSE) ## ----eval=TRUE------------------------------------------------------------- data("demoCircuit") rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 50, plots = FALSE, integrateStepSize = 0.1, simulationTime = 30) kd <- sRACIPE::sracipeKnockDown(rSet, plotToFile = FALSE, reduceProduction=50) ## ----eval=FALSE------------------------------------------------------------ # sRACIPE::sracipePlotCircuit(rSet, plotToFile = FALSE) ## ----eval=TRUE------------------------------------------------------------- rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20, initialNoise = 15, noiseScalingFactor = 0.1, nNoise = 2, plots = TRUE, plotToFile = FALSE, integrateStepSize = 0.1, simulationTime = 30) ## ----eval=TRUE------------------------------------------------------------- rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20, plots = FALSE, integrate = FALSE) params <- sRACIPE::sracipeParams(rSet) modifiedParams <- as.matrix(params) modifiedParams[,1] <- 0.1*modifiedParams[,1] sRACIPE::sracipeParams(rSet) <- DataFrame(modifiedParams) rSet <- sRACIPE::sracipeSimulate(rSet, plots = FALSE, genParams = FALSE) ## -------------------------------------------------------------------------- sessionInfo()