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waldronlab / TCGAutils

Toolbox package for organizing and working with TCGA data
https://bioconductor.org/packages/TCGAutils
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splitAssays(acc, sampleCodes = c("01", "10", "11")) fails #12

Closed lwaldron closed 6 years ago

lwaldron commented 6 years ago 
library(curatedTCGAData)
library(TCGAutils)
  acc <- curatedTCGAData("ACC",
                         assays = c("miRNASeqGene", "RPPAArray", "Mutation", "RNASeq2GeneNorm", "CNVSNP"),
                         dry.run = FALSE)
splitAssays(acc, sampleCodes = c("01", "10"))  #same for splitAssays(acc, sampleCodes = c("01", "10", "11"))
Error in TCGAsampleSelect(unlist(cnames, use.names = FALSE), scode) : 
  Inconsistent barcode lengths
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] TCGAutils_1.1.12            curatedTCGAData_1.3.3       MultiAssayExperiment_1.7.14
 [4] SummarizedExperiment_1.11.5 DelayedArray_0.7.19         BiocParallel_1.15.7        
 [7] matrixStats_0.53.1          Biobase_2.41.1              RaggedExperiment_1.5.2     
[10] GenomicRanges_1.33.6        GenomeInfoDb_1.17.1         IRanges_2.15.14            
[13] S4Vectors_0.19.17           BiocGenerics_0.27.1        

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4              purrr_0.2.5                   lattice_0.20-35              
 [4] htmltools_0.3.6               yaml_2.1.19                   interactiveDisplayBase_1.19.0
 [7] blob_1.1.1                    rlang_0.2.1                   later_0.7.3                  
[10] pillar_1.2.3                  glue_1.2.0                    DBI_1.0.0                    
[13] rappdirs_0.3.1                bit64_0.9-7                   bindrcpp_0.2.2               
[16] GenomeInfoDbData_1.1.0        bindr_0.1.1                   stringr_1.3.1                
[19] zlibbioc_1.27.0               ExperimentHub_1.7.1           rvest_0.3.2                  
[22] memoise_1.1.0                 knitr_1.20                    BiocInstaller_1.31.1         
[25] httpuv_1.4.4.2                curl_3.2                      AnnotationDbi_1.43.1         
[28] Rcpp_0.12.17                  xtable_1.8-2                  readr_1.1.1                  
[31] promises_1.0.1                jsonlite_1.5                  XVector_0.21.3               
[34] mime_0.5                      bit_1.1-14                    AnnotationHub_2.13.1         
[37] hms_0.4.2                     digest_0.6.15                 stringi_1.2.3                
[40] GenomicDataCommons_1.5.3      dplyr_0.7.6                   shiny_1.1.0                  
[43] grid_3.5.0                    tools_3.5.0                   bitops_1.0-6                 
[46] magrittr_1.5                  lazyeval_0.2.1                RCurl_1.95-4.10              
[49] tibble_1.4.2                  RSQLite_2.1.1                 pkgconfig_2.0.1              
[52] Matrix_1.2-14                 xml2_1.2.0                    assertthat_0.2.0             
[55] httr_1.3.1                    R6_2.2.2                      compiler_3.5.0               
>
LiNk-NY commented 6 years ago

It looks like the RPPA dataset has inconsistent barcodes: 

> vapply(colnames(acc), function(x) unique(nchar(x)), numeric(1L))
         ACC_CNVSNP-20160128    ACC_miRNASeqGene-20160128 
                          28                           28 
       ACC_Mutation-20160128 ACC_RNASeq2GeneNorm-20160128 
                          28                           28 
      ACC_RPPAArray-20160128 
                          27

I'll convert this error to a warning and try to create the sample table if possible.

Thanks, Marcel