> GDCdownload(query = query,

+             directory = DataDirectory)

Downloading data for project TCGA-STAD

GDCdownload will download 407 files. A total of 105.663384 MB

Downloading as: Sun_Aug__5_19_35_20_2018.tar.gz

Downloading: 110 MB     > 

> # 保存结果，方便后面使用

> data <- GDCprepare(query = query, 

+                        save = TRUE, 

+                        directory =  DataDirectory,

+                        save.filename = FileNameData)

|=================================================================| 100%    1 MB

  |======================================================================| 100%

Starting to add information to samples

 => Add clinical information to samples

Add FFPE information. More information at: 

=> https://cancergenome.nih.gov/cancersselected/biospeccriteria 

=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html

 => Adding subtype information to samples

stad subtype information from:doi:10.1038/nature13480

Error: $ operator is invalid for atomic vectors