TCGAbiolinks cannot find bcr_patient_barcode
1
0
Entering edit mode
Habil Zare ▴ 200
@habil-zare-7836
Last seen 11 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 • 1.5k views
ADD COMMENT
0
Entering edit mode

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.
ADD REPLY
0
Entering edit mode

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
ADD REPLY
2
Entering edit mode
@tiagochst-7121
Last seen 17 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"
    )
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

Just upgraded the version to 2.29.4 and commit to devel.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 540 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6