TCGAbiolinks download error

Question

[Björn]

I used following commands to download -"Data.category- Biospecimen"

bio_query <- GDCquery(project = "TCGA-PRAD", data.category = c("Biospecimen"))
GDCdownload(bio_query)

but received following error

Error in GDCdownload(bio_query) : We can only download one data type. Please use data.type argument in GDCquery to filter results.

My aim is to get the biospecimen, clinical.info="sample" data . How to solve the problem ? How to get the normal sample data for the TCGA-PRAD ?

Answer 1

[Mathias]

You need to add your data.type, that's all ;):

bio_query <- GDCquery(project = "TCGA-PRAD", data.category ="Biospecimen", data.type="Biospecimen Supplement")

Basically, if you specify Biospecimen in your data category in the TCGA repository, you'll see that it contains two datatypes. You had to specify which one you need. And that applies to everything you want to download, just go to the repository and make your query as specific as needs be ;)