## ----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--------------------------------------------------- # source("http://bioconductor.org/biocLite.R") # biocLite("rcellminer") # biocLite("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()