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Description
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:
▆
- ├─easyTCGA::getmrnaexpr("TCGA-GBM")
- │ └─TCGAbiolinks::GDCprepare(...)
- │ └─TCGAbiolinks:::readTranscriptomeProfiling(...)
- │ └─TCGAbiolinks:::makeSEfromTranscriptomeProfilingSTAR(...)
- │ └─TCGAbiolinks::colDataPrepare(cases)
- │ └─TCGAbiolinks:::splitAPICall(...)
- │ └─base::tryCatch(...)
- │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
- │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
- │ └─value[3L]
- │ ├─plyr::rbind.fill(info, FUN(items[start:end]))
- │ └─TCGAbiolinks (local) FUN(items[start:end])
- │ └─... %>% ...
- ├─dplyr::rename(., days_to_last_follow_up = days_to_follow_up)
- ├─dplyr::rename_at(...)
- │ └─dplyr:::tbl_at_vars(.tbl, .vars, .include_group_vars = TRUE)
- │ └─dplyr::tbl_vars(tbl)
- │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
- │ │ └─base::structure(...)
- │ └─dplyr:::tbl_vars_dispatch(x)
- ├─dplyr::ungroup(.)
- ├─dplyr::filter(., dplyr::row_number() == which.max(days_to_follow_up))
- ├─dplyr::group_by(., submitter_id)
- ├─dplyr::filter(., !is.na(submitter_id), !is.na(days_to_follow_up))
- ├─dplyr::select(., c(submitter_id, days_to_follow_up, disease_response))
- └─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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