## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("curatedTCGAData") ## ----include=TRUE,results="hide",message=FALSE,warning=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")) ## ----------------------------------------------------------------------------- tums <- TCGAsampleSelect(colnames(accmae), "01") ## ----------------------------------------------------------------------------- accmae[, tums, ] ## ----------------------------------------------------------------------------- td <- tempdir() tempd <- file.path(td, "ACCMAE") if (!dir.exists(tempd)) dir.create(tempd) exportClass(accmae, dir = tempd, fmt = "csv", ext = ".csv") ## ----------------------------------------------------------------------------- sessionInfo()