## ----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) ## ----eval=FALSE--------------------------------------------------------------- # citation("curatedTCGAData") # citation("MultiAssayExperiment") ## ----------------------------------------------------------------------------- head( curatedTCGAData( diseaseCode = "COAD", assays = "*", version = "1.1.38" ) ) ## ----------------------------------------------------------------------------- data('diseaseCodes', package = "TCGAutils") head(diseaseCodes) ## ----eval=FALSE--------------------------------------------------------------- # curatedTCGAData( # diseaseCode = "*", assays = "*", version = "2.0.1" # ) ## ----------------------------------------------------------------------------- head( curatedTCGAData( diseaseCode = "COAD", assays = "*", version = "2.0.1" ) ) ## ----message=FALSE------------------------------------------------------------ (accmae <- curatedTCGAData( "ACC", c("CN*", "Mutation"), version = "2.0.1", dry.run = FALSE )) ## ----------------------------------------------------------------------------- head(getSubtypeMap(accmae)) ## ----------------------------------------------------------------------------- head(getClinicalNames("ACC")) colData(accmae)[, getClinicalNames("ACC")][1:5, 1:5] ## ----------------------------------------------------------------------------- sampleTables(accmae) ## ----------------------------------------------------------------------------- data(sampleTypes, package = "TCGAutils") head(sampleTypes) ## ----------------------------------------------------------------------------- sampleTypes[sampleTypes[["Code"]] %in% c("01", "10"), ] TCGAsplitAssays(accmae, c("01", "10")) ## ----------------------------------------------------------------------------- tums <- TCGAsampleSelect(colnames(accmae), "01") ## ----------------------------------------------------------------------------- (primaryTumors <- TCGAprimaryTumors(accmae)) ## ----------------------------------------------------------------------------- sampleTables(primaryTumors) ## ----------------------------------------------------------------------------- (accmut <- getWithColData(accmae, "ACC_Mutation-20160128", mode = "append")) head(colData(accmut)[, 1:4]) ## ----------------------------------------------------------------------------- ragex <- accmae[["ACC_Mutation-20160128"]] ## convert score to numeric mcols(ragex)$Entrez_Gene_Id <- as.numeric(mcols(ragex)[["Entrez_Gene_Id"]]) sparseAssay(ragex, i = "Entrez_Gene_Id", sparse=TRUE)[1:6, 1:3] ## ----------------------------------------------------------------------------- as(ragex, "GRangesList") ## ----------------------------------------------------------------------------- td <- tempdir() tempd <- file.path(td, "ACCMAE") if (!dir.exists(tempd)) dir.create(tempd) exportClass(accmae, dir = tempd, fmt = "csv", ext = ".csv") ## ----------------------------------------------------------------------------- sessionInfo()