## ----knitrSetup, include=FALSE-------------------------------------------
library(knitr)
opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center", tidy=TRUE)

## ----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---------------------------------------------------------
sessionInfo()