## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set( concordance=TRUE ) ## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set( concordance=TRUE ) ## ----load.package, echo=FALSE, warning=FALSE, message=FALSE---- options(width=60) library(synergyfinder) ## ----loading.data----------------------------------------- data("mathews_screening_data") head(mathews_screening_data) ## --------------------------------------------------------- # Set the random number seed for generating noises. set.seed(1) dose.response.mat <- ReshapeData(mathews_screening_data, data.type = "viability", impute = TRUE, noise = TRUE, correction = "non") ## --------------------------------------------------------- str(dose.response.mat) ## ----fig.show='hide'-------------------------------------- PlotDoseResponse(dose.response.mat) ## ----fig.show='hide'-------------------------------------- PlotDoseResponse(dose.response.mat, save.file = TRUE) ## --------------------------------------------------------- synergy.score <- CalculateSynergy(data = dose.response.mat, method = "ZIP") ## --------------------------------------------------------- str(synergy.score) ## ----fig.show='hide'-------------------------------------- PlotSynergy(synergy.score, type = "all", save.file = TRUE)