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.
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
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.