GDCprepare error in TARGET-AML data access

Question

[Beth]

Hello there,

I am trying to access the STAR-Counts files from TARGET-AML 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.

Backtrace data (rlang::last_error()):

1. TCGAbiolinks::GDCprepare(queryDown_Target2)
2. purrr::map_dfc(., .f = function(y) y[, 2:4])
3. purrr::map(.x, .f, ...)
4. TCGAbiolinks .f(.x[[i]], ...)
5. tibble:::[.tbl_df(y, , 2:4)
6. tibble:::vectbl_as_col_location(...)

Thank you in advance for your help!

P.S. GDCprepare still works with TCGA data.

[Kevin Blighe]

Cross-posted: https://support.bioconductor.org/p/9143546/