Is it possible to access controlled TCGA data through TCGA Biolinks in R?

Question

[Destiny]

I have access to controlled TCGA data but I am struggling to find the most efficient way to download and access the data in RStudio. Previously, I was able to use TCGA Biolinks to access open data. I learned from online resources that you can input an argument for your token file and use method = "client" to get access to the controlled data. However, I keep getting an error:

Error in download.file(url, ...) : cannot open URL '/system/files/public/file/gdc-client_v1.6.1_Windows_x64.zip'

and I'm not sure how to resolve it. Here is my code for what I have done up to this point:

query2_TCGA = GDCquery(
  project = "TCGA-CESC",
  data.category = "Simple Nucleotide Variation",
  experimental.strategy = "WXS",
  data.type = "Raw Simple Somatic Mutation",
  workflow.type = "VarScan2")

query2_TCGA

token = read.delim("~/tokenfile.txt")

getManifest(query2_TCGA)
GDCdownload(query = query2_TCGA,
            token.file=token,
            method = "client")

If there is a problem with my code, please let me know! Otherwise, what would you recommend for downloading and opening controlled TCGA data in RStudio? Thank you so much!

Edit: to fix the syntax for calling the token file.

[GenoMax]

Can you confirm that you have a token file i.e. permission to access controlled data.

This seems useful: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/319

[Destiny]

Hi, I have a token file downloaded from the GDC portal and fixed the syntax to be token.file = "filenamefortoken.txt", but I am still receiving the error.

Answer 1

[Destiny]

For future reference, yes, it is possible! MacOS users seem to have no problem. Download the GDC client from the GDC website, and the above code should work. As of right now, after a conversation with someone from the GDC, it seems to be a problem only with Windows computers, so hopefully, a solution will be released soon. Note: The GDC client should still work fine on its own.