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Hello, I've been recently trying to download clinical data from TCGA using the TCGAbiolinks package, but I get an error when running the following code:
clinical_data <- GDCquery_clinic(project = "TCGA-TGCT", type = "clinical")
# it gives the following error
Error in set(x, j = name, value = value): Supplied 263 items to be assigned to 338 items of column 'submitter_id'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.
Can anyone give any advice on how to fix this or alternative ways to download the clinical data, most importantly the primary diagnoses of the patients?
I was having the same problem. You can check the answer in a previous post.
Specifically, reinstalling the devel version from GitHub allowed it to work for me again.
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical data.