Always it is recommended to show what you have tried, your code and ....
Just to write something helpful, here are codes for downloading a cancer expression matrix and associated clinical data using
require(TCGAbiolinks) require(SummarizedExperiment) query <- GDCquery(project = "TCGA-BLCA", # the TCGA name for your cancer data.category = "Gene expression", data.type = "Gene expression quantification", platform = "Illumina HiSeq", file.type = "normalized_results", experimental.strategy = "RNA-Seq", legacy = TRUE) GDCdownload(query, method = "api") dat <- GDCprepare(query = query, save = TRUE, save.filename = "exp.rda") rna <- as.data.frame(SummarizedExperiment::assay(dat)) # exp matrix clinical <- data.frame([email protected]) # associated clinical data
You can get access to the S4 object using the package
SummarizedExperiment, different functions. Here I used the
assay function from this package to make a data frame out of the expression matrix.