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I want to use GDCprepare for data with STAR - counts workflow in TCGAbiolinks package. It gives me error :
Error in `fn()`:
! Join columns must be present in data.
x Problem with `#gene`.
Run `rlang::last_error()` to see where the error occurred
my function command is :
query <- GDCquery(
project = "TCGA-SKCM",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts")
GDCdownload(query)
prep <- GDCprepare(query)
the GDCprepare is aborted in the end of the process. I don't know what the problem is. does anyone know ?
Please, do you have the latest version 2.25.0 installed?
BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")