UUIDtoBarcode returns <0 rows> (or 0-length row.names)

[jorisvdhaar]

I'm trying to retrieve TCGA barcodes using UUIDs for RNAseq data obtained from GDC, but without success.

library(TCGAutils)
id_vector = c('0341a31a-3514-402a-89b8-b225a79a3fba', '0447c027-b853-4940-b4bb-42f01ece8bb8')

UUIDtoBarcode(id_vector, id_type = c("case_id", "file_id"), end_point = "sample", legacy = TRUE)

[1] case_id      submitter_id
<0 rows> (or 0-length row.names)

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /home/j.vd.haar/anaconda3/lib/R/lib/libRblas.so
LAPACK: /home/j.vd.haar/anaconda3/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] TCGAutils_1.2.1

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.12.0 progress_1.2.0             
 [3] tidyselect_0.2.5            purrr_0.2.5                
 [5] lattice_0.20-38             stats4_3.5.0               
 [7] rtracklayer_1.42.0          GenomicFeatures_1.34.1     
 [9] blob_1.1.1                  XML_3.98-1.16              
[11] rlang_0.3.0.1               pillar_1.3.0               
[13] glue_1.3.0                  DBI_1.0.0                  
[15] BiocParallel_1.16.0         rappdirs_0.3.1             
[17] BiocGenerics_0.28.0         bit64_0.9-7                
[19] bindrcpp_0.2.2              matrixStats_0.54.0         
[21] GenomeInfoDbData_1.2.0      bindr_0.1.1                
[23] stringr_1.3.1               zlibbioc_1.28.0            
[25] Biostrings_2.50.1           rvest_0.3.2                
[27] memoise_1.1.0               Biobase_2.42.0             
[29] IRanges_2.16.0              biomaRt_2.38.0             
[31] MultiAssayExperiment_1.8.1  GenomeInfoDb_1.18.1        
[33] curl_3.2                    parallel_3.5.0             
[35] AnnotationDbi_1.44.0        Rcpp_1.0.0                 
[37] readr_1.1.1                 DelayedArray_0.8.0         
[39] S4Vectors_0.20.1            jsonlite_1.5               
[41] XVector_0.22.0              bit_1.1-14                 
[43] Rsamtools_1.34.0            hms_0.4.2                  
[45] digest_0.6.18               stringi_1.2.4              
[47] GenomicDataCommons_1.6.0    dplyr_0.7.8                
[49] GenomicRanges_1.34.0        grid_3.5.0                 
[51] tools_3.5.0                 bitops_1.0-6               
[53] magrittr_1.5                RCurl_1.95-4.11            
[55] lazyeval_0.2.1              RSQLite_2.1.1              
[57] tibble_1.4.2                crayon_1.3.4               
[59] pkgconfig_2.0.2             Matrix_1.2-15              
[61] xml2_1.2.0                  prettyunits_1.0.2          
[63] assertthat_0.2.0            httr_1.3.1                 
[65] R6_2.3.0                    GenomicAlignments_1.18.0   
[67] compiler_3.5.0             
> 

Would be great if you could help me out!

Cheers, Joris

[LiNk-NY]

It seems like you misspecified the function call. Are you sure it is legacy data? This worked for me:

UUIDtoBarcode(id_vector, id_type = "file_id", end_point = "sample", legacy = FALSE)

Best regards, Marcel

[jorisvdhaar]

You're absolutely right, Marcel. Thanks a lot!