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Add clinical information to samples:Column disease_response doesn't exist. #649

@smallboy-code

Description

@smallboy-code

When run:
library(easyTCGA)
getmrnaexpr("TCGA-GBM")

It occur the error in dplyr::select():
! Can't select columns that don't exist.
✖ Column disease_response doesn't exist.
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace()
<error/vctrs_error_subscript_oob>
Error in dplyr::select():
! Can't select columns that don't exist.
✖ Column disease_response doesn't exist.

Backtrace:

  1. ├─easyTCGA::getmrnaexpr("TCGA-GBM")
  2. │ └─TCGAbiolinks::GDCprepare(...)
  3. │ └─TCGAbiolinks:::readTranscriptomeProfiling(...)
  4. │ └─TCGAbiolinks:::makeSEfromTranscriptomeProfilingSTAR(...)
  5. │ └─TCGAbiolinks::colDataPrepare(cases)
  6. │ └─TCGAbiolinks:::splitAPICall(...)
  7. │ └─base::tryCatch(...)
  8. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10. │ └─value[3L]
  11. │ ├─plyr::rbind.fill(info, FUN(items[start:end]))
  12. │ └─TCGAbiolinks (local) FUN(items[start:end])
  13. │ └─... %>% ...
  14. ├─dplyr::rename(., days_to_last_follow_up = days_to_follow_up)
  15. ├─dplyr::rename_at(...)
  16. │ └─dplyr:::tbl_at_vars(.tbl, .vars, .include_group_vars = TRUE)
  17. │ └─dplyr::tbl_vars(tbl)
  18. │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
  19. │ │ └─base::structure(...)
  20. │ └─dplyr:::tbl_vars_dispatch(x)
  21. ├─dplyr::ungroup(.)
  22. ├─dplyr::filter(., dplyr::row_number() == which.max(days_to_follow_up))
  23. ├─dplyr::group_by(., submitter_id)
  24. ├─dplyr::filter(., !is.na(submitter_id), !is.na(days_to_follow_up))
  25. ├─dplyr::select(., c(submitter_id, days_to_follow_up, disease_response))
  26. └─dplyr:::select.data.frame(., c(submitter_id, days_to_follow_up, disease_response))
    Run rlang::last_trace(drop = FALSE) to see 20 hidden frames.

Maybe the version of TCGAbiolinks needs to update?

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