## ----knitrSetup, include=FALSE------------------------------------------------ library(knitr) opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center", tidy=TRUE, eval=FALSE) ## ----install, eval=FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rcellminer") # BiocManager::install("rcellminerData") ## ----loadLibrary, message=FALSE, warning=FALSE-------------------------------- # library(rcellminer) # library(rcellminerData) ## ----searchHelp, eval=FALSE, tidy=FALSE--------------------------------------- # help.search("rcellminerData") ## ----getDataHelp, eval=FALSE, tidy=FALSE-------------------------------------- # help("drugData") # help("molData") ## ----------------------------------------------------------------------------- # # Get the types of feature data in a MolData object. # names(getAllFeatureData(molData)) ## ----------------------------------------------------------------------------- # class(molData[["exp"]]) # # geneExpMat <- exprs(molData[["exp"]]) ## ----------------------------------------------------------------------------- # getSampleData(molData)[1:10, "TissueType"] ## ----------------------------------------------------------------------------- # # Add data # molData[["test"]] <- molData[["pro"]] # # names(getAllFeatureData(molData)) ## ----------------------------------------------------------------------------- # drugActMat <- exprs(getAct(drugData)) # dim(drugActMat) # # drugRepeatActMat <- exprs(getRepeatAct(drugData)) # dim(drugRepeatActMat) ## ----------------------------------------------------------------------------- # drugAnnotDf <- as(featureData(getAct(drugData)), "data.frame") # # colnames(drugAnnotDf) ## ----------------------------------------------------------------------------- # identical(getSampleData(molData), getSampleData(drugData)) ## ----sessionInfo, eval=TRUE--------------------------------------------------- sessionInfo()