TCGAbiolinks cannot find bcr_patient_barcode
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Habil Zare ▴ 170
@habil-zare-7836
Last seen 3 months ago
United States/Austin Area

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.
TCGAbiolinks • 598 views
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Tracing:

> rlang::last_trace()
<error/rlang_error>
Error in `dplyr::group_by()`:
! Must group by variables found in `.data`.
Column `bcr_patient_barcode` is not found.
---
Backtrace:
 1. TCGAbiolinks::GDCprepare_clinic(query, directory = ".", clinical.info = "patient")
 2. followup %>% dplyr::group_by(bcr_patient_barcode) %>% ...
 3. dplyr::summarise(...)
 4. dplyr::group_by(., bcr_patient_barcode)
 5. dplyr:::group_by.data.frame(., bcr_patient_barcode)
Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.
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I use Version 2.29.3.

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] TCGAbiolinks_2.29.3

loaded via a namespace (and not attached):
 [1] KEGGREST_1.40.0             SummarizedExperiment_1.30.1
 [3] gtable_0.3.3                xfun_0.39                  
 [5] ggplot2_3.4.2               TCGAbiolinksGUI.data_1.20.0
 [7] Biobase_2.60.0              lattice_0.21-8             
 [9] tzdb_0.4.0                  vctrs_0.6.2                
[11] tools_4.3.0                 bitops_1.0-7               
[13] generics_0.1.3              curl_5.0.0                 
[15] stats4_4.3.0                tibble_3.2.1               
[17] fansi_1.0.4                 AnnotationDbi_1.62.1       
[19] RSQLite_2.3.1               blob_1.2.4                 
[21] pkgconfig_2.0.3             Matrix_1.5-4               
[23] data.table_1.14.8           dbplyr_2.3.2               
[25] S4Vectors_0.38.1            lifecycle_1.0.3            
[27] GenomeInfoDbData_1.2.10     compiler_4.3.0             
[29] stringr_1.5.0               progress_1.2.2             
[31] Biostrings_2.68.0           munsell_0.5.0              
[33] GenomeInfoDb_1.36.0         RCurl_1.98-1.12            
[35] tidyr_1.3.0                 pillar_1.9.0               
[37] crayon_1.5.2                DelayedArray_0.26.2        
[39] cachem_1.0.8                rvest_1.0.3                
[41] digest_0.6.31               tidyselect_1.2.0           
[43] stringi_1.7.12              purrr_1.0.1                
[45] dplyr_1.1.2                 biomaRt_2.56.0             
[47] fastmap_1.1.1               grid_4.3.0                 
[49] colorspace_2.1-0            cli_3.6.1                  
[51] magrittr_2.0.3              S4Arrays_1.0.4             
[53] XML_3.99-0.14               utf8_1.2.3                 
[55] withr_2.5.0                 readr_2.1.4                
[57] rappdirs_0.3.3              filelock_1.0.2             
[59] prettyunits_1.1.1           scales_1.2.1               
[61] bit64_4.0.5                 XVector_0.40.0             
[63] httr_1.4.6                  matrixStats_0.63.0         
[65] bit_4.0.5                   png_0.1-8                  
[67] hms_1.1.3                   memoise_2.0.1              
[69] knitr_1.42                  GenomicRanges_1.52.0       
[71] IRanges_2.34.0              BiocFileCache_2.8.0        
[73] rlang_1.1.1                 Rcpp_1.0.10                
[75] glue_1.6.2                  DBI_1.1.3                  
[77] downloader_0.4              xml2_1.3.4                 
[79] BiocGenerics_0.46.0         jsonlite_1.8.4             
[81] plyr_1.8.8                  R6_2.5.1                   
[83] MatrixGenerics_1.12.0       zlibbioc_1.46.0
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@tiagochst-7121
Last seen 3 months ago
Miami, US

Please, could you update the package with the GitHub version devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks",ref = "devel")

There is no follow up information in the XML files for TCGA-LAML.

query <- GDCquery(
        project = "TCGA-LAML",
        data.category = "Clinical",
        data.format = "bcr xml"
    )

    GDCdownload(
        query = query,
        directory = "."
    )

    clinical <- GDCprepare_clinic(
        query = query,
        directory = ".",
        clinical.info = "patient"
    )
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Thanks Tiago C. Silva ! The code you sent me worked here, however, I need TCGAbiolinks for another package that I developed for Bioconductor and I cannot depend on this version on GitHub. When do you think it will be available on Bioconductor devel?

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I already pushed the changes to Bioconductor, probably in a few days.

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Have you increased the version so that it builds anew? I just tried your code with the 2.29.3 version from Bioconductor dev. and I got the same error.

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Just upgraded the version to 2.29.4 and commit to devel.

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I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!

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