Hello there,

I am trying to access the STAR-Counts files from TARGET-AML (they using STAR instead HTSeq-counts now) using TCGAbiolinks. When using the GDCprepare function (see example below), an error occurs that I don't know how to fix (there were no problems with GDCprepare before).

queryDown_Target2 <- GDCquery(project = "TARGET-AML", 
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification", 
                      workflow.type = "STAR - Counts", 
                      barcode = c("TARGET-20-PASPLU-04A-01R"))

Then I try to load the files and use GDCprepare:

GDCdownload(queryDown_Target2)
data2 <- GDCprepare(queryDown_Target2)

And I get this error:

Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
ℹ Locations 2, 3, and 4 don't exist.
ℹ There is only 1 column.

P.S. GDCprepare still works with TCGA data.

Please, update to the latest version of the package from GitHub. The code is working on my side.

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")