TCGAbiolinks download error
1
0
Entering edit mode
3.4 years ago
Björn ▴ 100

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 ?

tcga tcgabiolinks R • 1.4k views
ADD COMMENT
2
Entering edit mode
3.4 years ago
Mathias ▴ 90

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 ;)

ADD COMMENT

Login before adding your answer.

Traffic: 1648 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6