## ---- echo = FALSE, warning = FALSE----------------------------------------
suppressPackageStartupMessages({
    library(MultiAssayExperiment)
    library(curatedTCGAData)
    library(TCGAutils)
})

## ---- eval=FALSE-----------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("curatedTCGAData")

## ---- eval = FALSE---------------------------------------------------------
#  library(curatedTCGAData)
#  library(MultiAssayExperiment)
#  library(TCGAutils)

## --------------------------------------------------------------------------
curatedTCGAData(diseaseCode = "*", assays = "*", dry.run = TRUE)

## --------------------------------------------------------------------------
curatedTCGAData(diseaseCode = "COAD", assays = "RPPA*", dry.run = TRUE)

## ---- message=FALSE--------------------------------------------------------
(accmae <- curatedTCGAData("ACC", c("CN*", "Mutation"), FALSE))

## --------------------------------------------------------------------------
head(getSubtypeMap(accmae))

## --------------------------------------------------------------------------
head(getClinicalNames("ACC"))

colData(accmae)[, getClinicalNames("ACC")][1:5, 1:5]

## --------------------------------------------------------------------------
sampleTables(accmae)

## --------------------------------------------------------------------------
sampleTypes[sampleTypes[["Code"]] %in% c("01", "10"), ]

splitAssays(accmae, c("01", "10"))