Is it possible to access controlled TCGA data through TCGA Biolinks in R?
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9 days ago
Destiny • 0

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,
            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!

R GDC RStudio TCGA • 201 views
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Entering edit mode

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

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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.

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