GCD query Error

[Pmgranjo]

When I try to retrieve Gene Expression Data through this code:

query$rnaseq <- GDCquery(project = project, data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts") GDCdownload(query$rnaseq, method = 'api') gdc$rnaseq <- GDCprepare(query$rnaseq) save(gdc, query, file = cached.file)

The following error appears

Error in y[, 2:4]: ! Can't subset columns past the end. i Locations 2, 3, and 4 don't exist. i There is only 1 column.

Backtrace: x

1. +-TCGAbiolinks::GDCprepare(query$rnaseq)
2. | -TCGAbiolinks:::readTranscriptomeProfiling(...)
3. | +-base::suppressMessages(...)
4. | | -base::withCallingHandlers(...)
5. | -x %>% map_dfc(.f = function(y) y[, 2:4])
6. -purrr::map_dfc(., .f = function(y) y[, 2:4])
7. -purrr::map(.x, .f, ...)
8. -TCGAbiolinks (local) .f(.x[[i]], ...)
9. +-y[, 2:4]
   10. +-readr:::[.spec_tbl_df(y, , 2:4)
   11. +-base::NextMethod([)
   12. -tibble:::[.tbl_df(y, , 2:4)****
   13. -tibble:::vectbl_as_col_location(...)
   14. +-tibble:::subclass_col_index_errors(...)
   15. | -base::withCallingHandlers(...)
   16. -vctrs::vec_as_location(j, n, names, call = call)
   17. -vctrs (local) <fn>()
   18. -vctrs:::stop_subscript_oob(...)
   19. -vctrs:::stop_subscript(...)
   20. -rlang::abort(...)

My error is highlighted with ***

[tiagochst]

@Pmgranjo what is the project argument ?

[cbravo93]

I am also getting this error, with any project name I use (e.g. TCGA-CHOL). Did you manage to solve it?

Thanks!

Carmen

[tiagochst]

@cbravo93 What is the version of TCGAbiolinks you have installed ? The following code is working on version 2.25.3.

library(TCGAbiolinks)
query <- GDCquery(
  project = "TCGA-CHOL",
  data.category = "Transcriptome Profiling",
  data.type = "Gene Expression Quantification",
  workflow.type = "STAR - Counts"
)
GDCdownload(query, method = 'api',files.per.chunk = 10)
gdc <- GDCprepare(query)

[cbravo93]

Hi @tiagochst !

Thanks for the quick repsonse! I am using 2.25.4, I will try downgrading. Which versions of tidyverse/purr are you using just in case it comes from there?

Thanks!

C

[cbravo93]

Quick update, I just installed from Github to check the newest version (2.27.2) and it works with this version as well. Thanks!