Issue with TCGAbiolinks package.
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0
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@salvocomplicazioni1-14125
Last seen 22 months ago

I'm trying to download copy number variation file with TCGAbiolinks package and following code:


library(TCGAbiolinks)
Tumor <- c("BLCA)
query <- GDCquery(project = paste("TCGA-",Tumor, sep = ""),
                  data.category = "Copy Number Variation",
                  data.type = "Gene Level Copy Number Scores",              
                  access="open")
GDCdownload(query, directory = "/tank/home/SIG/")
data <- GDCprepare(query, directory = "/tank/home/SIG/")

but when i run GDCprepare I get an error:

Reading GISTIC file
Parsed with column specification:
cols(
  .default = col_double(),
  `Gene Symbol` = col_character(),
  Cytoband = col_character()
)
See spec(...) for full column specifications.
Error in stri_split_regex(string, pattern, n = n, simplify = simplify,  : 
  oggetto "res" non trovato
TCGA GDCprepare • 434 views
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Entering edit mode

Can you update your post to include the output of sessionInfo() so we can see which versions of R and TCGAbiolinks you're using. I get errors earlier in your example code with my setup:

> library(TCGAbiolinks)
> Tumor <- c("BLCA")
> query <- GDCquery(project = paste("TCGA-",Tumor, sep = ""),
+                   data.category = "Copy Number Variation",
+                   data.type = "Gene Level Copy Number Scores",              
+                   access="open")
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38


|sort(harmonized.data.type)        |
|:---------------------------------|
|Biospecimen Supplement            |
|Clinical Supplement               |
|Copy Number Segment               |
|Gene Expression Quantification    |
|Isoform Expression Quantification |
|Masked Copy Number Segment        |
|Masked Somatic Mutation           |
|miRNA Expression Quantification   |
Error in checkDataTypeInput(legacy = legacy, data.type = data.type) : 
  Please set a data.type argument from the column harmonized.data.type above
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /g/easybuild/x86_64/CentOS/7/haswell/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.so

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

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

other attached packages:
[1] TCGAbiolinks_2.8.3

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            selectr_0.4-1               rjson_0.2.20               
  [4] hwriter_1.3.2               circlize_0.4.4              XVector_0.22.0             
  [7] GenomicRanges_1.34.0        GlobalOptions_0.1.0         rstudioapi_0.9.0           
... 
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> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
 [1] reshape2_1.4.3                         BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 DT_0.5                                 TCGAbiolinks_2.10.2                   
 [5] BSgenome.Mmusculus.UCSC.mm9_1.4.0      BSgenome_1.50.0                        rtracklayer_1.42.1                     Biostrings_2.50.2                     
 [9] XVector_0.22.0                         deconstructSigs_1.8.0                  reprex_0.2.1                           calibrate_1.7.2                       
[13] MASS_7.3-51.1                          RColorBrewer_1.1-2                     bindrcpp_0.2.2                         pathview_1.22.1                       
[17] org.Hs.eg.db_3.7.0                     AnnotationDbi_1.44.0                   shinyBS_0.61                           shinydashboard_0.7.1                  
[21] shinyjs_1.0                            jsonlite_1.6                           shiny_1.2.0                            plotly_4.8.0                          
[25] debrowser_1.10.9                       biomaRt_2.38.0                         CEMiTool_1.6.10                        forcats_0.3.0                         
[29] stringr_1.3.1                          dplyr_0.7.8                            purrr_0.3.0                            readr_1.3.1                           
[33] tidyr_0.8.2                            tibble_2.0.1                           tidyverse_1.2.1                        genefilter_1.64.0                     
[37] hexbin_1.27.2                          splitstackshape_1.4.6                  vsn_3.50.0                             gplots_3.0.1.1                        
[41] ggplot2_3.1.0                          magrittr_1.5                           DESeq2_1.22.2                          SummarizedExperiment_1.12.0           
[45] DelayedArray_0.8.0                     BiocParallel_1.16.5                    matrixStats_0.54.0                     Biobase_2.42.0                        
[49] GenomicRanges_1.34.0                   GenomeInfoDb_1.18.1                    IRanges_2.16.0                         S4Vectors_0.20.1                      
[53] BiocGenerics_0.28.0                    R.utils_2.7.0                          R.oo_1.22.0                            R.methodsS3_1.7.1                     

loaded via a namespace (and not attached):
  [1] statnet.common_4.2.0        Hmisc_4.2-0                 class_7.3-15                Rsamtools_1.34.1            foreach_1.4.4              
  [6] crayon_1.3.4                nlme_3.1-137                backports_1.1.3             sva_3.30.1                  colourpicker_1.0           
 [11] impute_1.56.0               GOSemSim_2.8.0              rlang_0.3.1                 readxl_1.2.0                intergraph_2.0-2           
 [16] limma_3.38.3                rjson_0.2.20                cmprsk_2.2-7                bit64_0.9-7                 glue_1.3.0                 
 [21] trimcluster_0.1-2.1         UpSetR_1.3.3                DOSE_3.8.2                  haven_2.0.0                 tidyselect_0.2.5           
 [26] km.ci_0.5-2                 XML_3.98-1.16               zoo_1.8-4                   ggpubr_0.2                  GenomicAlignments_1.18.1   
 [31] org.Mm.eg.db_3.7.0          xtable_1.8-3                evaluate_0.12               cli_1.0.1                   zlibbioc_1.28.0            
 [36] hwriter_1.3.2               rstudioapi_0.9.0            miniUI_0.1.1.1              whisker_0.3-2               gRbase_1.8-3.4             
 [41] rpart_4.1-13                fastmatch_1.1-0             xfun_0.4                    cluster_2.0.7-1               BiocManager_1.30.4            

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I found in readGISTIC function:

else if (grepl("Copy Number Variation", query$data.category, 
    ignore.case = TRUE)) {
    if (query$data.type == "Gene Level Copy Number Scores") {
      data <- readGISTIC(files, res$results[[1]]$cases)
    }
    else {
      data <- readCopyNumberVariation(files, query$results[[1]]$cases)
    }
  }

but the following object doesn't seems to exists.

res$results[[1]]$cases

If I modify it as following:

query$results[[1]]$cases

The code works fine. Is it possible?

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Mike Smith ★ 5.0k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

It looks like this was a bug that was fixed a few weeks ago (https://github.com/BioinformaticsFMRP/TCGAbiolinks/commit/8c5449958ad2e1cd300daa033d57d1267e7c9d6d)

I would do a BiocManager::install('TCGAbiolinks') to get version 2.10.3 and try from there.

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Yes, TCGAbiolinks version 2.10.3 fix the issue.

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