## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(progress = FALSE)

## ----message=FALSE, warning=FALSE, include=FALSE-------------------------
library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)

## ----results = 'hide', message=FALSE, warning=FALSE, eval = FALSE--------
#  query <- GDCquery(project = "TCGA-GBM",
#                             data.category = "Gene expression",
#                             data.type = "Gene expression quantification",
#                             platform = "Illumina HiSeq",
#                             file.type  = "normalized_results",
#                             experimental.strategy = "RNA-Seq",
#                             barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
#                             legacy = TRUE)
#  GDCdownload(query, method = "api", chunks.per.download = 10)
#  data <- GDCprepare(query)

## ----message=FALSE, warning=FALSE, eval = FALSE--------------------------
#  # Gene expression aligned against hg19.
#  datatable(as.data.frame(colData(data)),
#                options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
#                rownames = FALSE)
#  # Only first 100 to make render faster
#  datatable(assay(data)[1:100,],
#                options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
#                rownames = TRUE)
#  
#  rowRanges(data)

## ----results = 'hide',eval = FALSE, message=FALSE, warning=FALSE---------
#  # Gene expression aligned against hg38
#  query <- GDCquery(project = "TCGA-GBM",
#                    data.category = "Transcriptome Profiling",
#                    data.type = "Gene Expression Quantification",
#                    workflow.type = "HTSeq - Counts",
#                    barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"))
#  tryCatch(GDCdownload(query, method = "client"),error = function(e)GDCdownload(query))
#  data <- GDCprepare(query)