Hi TCGAbiolinks Team,
Thanks for your useful package. I get the following error while getting clinical data from the TCGA-LAML project. This issue did not exist in the former versions of TCGAbiolinks where you had allowed using legacy. Do you think it can be fixed soon?
library(TCGAbiolinks) query <- GDCquery(project="TCGA-LAML", data.category="Clinical", file.type="xml") GDCdownload(query, directory=".") clinical <- GDCprepare_clinic(query,directory=".",clinical.info="patient")
I got the following error message:
|======================================================================| 100% To get the following information please change the clinical.info argument => new_tumor_events: new_tumor_event => drugs: drug => follow_ups: follow_up => radiations: radiation Updating days_to_last_followup and vital_status from follow_up information using last entry Error in `dplyr::group_by()`: ! Must group by variables found in `.data`. Column `bcr_patient_barcode` is not found. Run `rlang::last_trace()` to see where the error occurred.
I use Version 2.29.3.