Question: Downloading bt.exon_quantification with TCGAbiolinks
0
gravatar for Marcel Ramos
3.5 years ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

Hi there,

I am trying to download the "bt.exon_quantification" files using TCGAbiolinks but I'm running into a bug:

library(TCGAbiolinks)
prad <- TCGAquery(tumor = "prad", platform = "IlluminaHiSeq_RNASeqV2", level = 3)
TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification")

returns the error message: 

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
| Downloading:550 files
| Path:~/Documents/rawdata//unc.edu_PRAD.IlluminaHiSeq_RNASeqV2.Level_3.1.14.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
  |                                                                              |   0%
Error in if (force || !file.exists(file.path(path, folder, files[i])) ||  :
  missing value where TRUE/FALSE needed
traceback()
1: TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification")
sessionInfo()
R Under development (unstable) (2015-11-25 r69695)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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] TCGAbiolinks_1.1.26

loaded via a namespace (and not attached):
  [1] circlize_0.3.5                          aroma.light_3.1.1                       plyr_1.8.3                             
  [4] igraph_1.0.1                            ConsensusClusterPlus_1.35.0             splines_3.3.0                          
  [7] BiocParallel_1.5.21                     GenomeInfoDb_1.7.6                      ggplot2_2.1.0                          
 [10] TH.data_1.0-7                           digest_0.6.9                            foreach_1.4.3                          
 [13] BiocInstaller_1.21.4                    rsconnect_0.4.2.1                       gdata_2.17.0                           
 [16] magrittr_1.5                            memoise_1.0.0                           cluster_2.0.3                          
 [19] doParallel_1.0.10                       limma_3.27.15                           ComplexHeatmap_1.9.5                   
 [22] Biostrings_2.39.12                      annotate_1.49.1                         matrixStats_0.50.1                     
 [25] R.utils_2.3.0                           sandwich_2.3-4                          colorspace_1.2-6                       
 [28] rvest_0.3.1                             ggrepel_0.5                             haven_0.2.0                            
 [31] dplyr_0.4.3                             RCurl_1.95-4.8                          hexbin_1.27.1                          
 [34] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 graph_1.49.1                            genefilter_1.53.3                      
 [37] lme4_1.1-11                             supraHex_1.9.0                          survival_2.38-3                        
 [40] zoo_1.7-12                              iterators_1.0.8                         ape_3.4                                
 [43] gtable_0.2.0                            zlibbioc_1.17.1                         XVector_0.11.8                         
 [46] MatrixModels_0.4-1                      GetoptLong_0.1.2                        sjmisc_1.7                             
 [49] car_2.1-2                               Rgraphviz_2.15.0                        shape_1.4.2                            
 [52] BiocGenerics_0.17.5                     SparseM_1.7                             scales_0.4.0                           
 [55] DESeq_1.23.1                            mvtnorm_1.0-5                           DBI_0.3.1                              
 [58] GGally_1.0.1                            edgeR_3.13.8                            Rcpp_0.12.4                            
 [61] xtable_1.8-2                            matlab_1.0.2                            preprocessCore_1.33.0                  
 [64] stats4_3.3.0                            httr_1.1.0                              gplots_3.0.1                           
 [67] RColorBrewer_1.1-2                      modeltools_0.2-21                       reshape_0.8.5                          
 [70] XML_3.98-1.4                            R.methodsS3_1.7.1                       nnet_7.3-12                            
 [73] reshape2_1.4.1                          AnnotationDbi_1.33.8                    munsell_0.4.3                          
 [76] tools_3.3.0                             downloader_0.4                          RSQLite_1.0.0                          
 [79] devtools_1.11.0                         stringr_1.0.0                           knitr_1.12.3                           
 [82] caTools_1.17.1                          dendextend_1.1.8                        coin_1.1-2                             
 [85] EDASeq_2.5.1                            nlme_3.1-126                            quantreg_5.21                          
 [88] whisker_0.3-2                           R.oo_1.20.0                             xml2_0.1.2                             
 [91] biomaRt_2.27.2                          pbkrtest_0.4-6                          curl_0.9.7                             
 [94] affyio_1.41.0                           geneplotter_1.49.0                      stringi_1.0-1                          
 [97] GenomicFeatures_1.23.27                 lattice_0.20-33                         Matrix_1.2-4                           
[100] psych_1.5.8                             nloptr_1.0.4                            effects_3.1-1                          
[103] stringdist_0.9.4.1                      GlobalOptions_0.0.9                     data.table_1.9.6                       
[106] cowplot_0.6.1                           bitops_1.0-6                            dnet_1.0.8                             
[109] rtracklayer_1.31.10                     GenomicRanges_1.23.25                   R6_2.1.2                               
[112] latticeExtra_0.6-28                     affy_1.49.0                             hwriter_1.3.2                          
[115] ShortRead_1.29.2                        KernSmooth_2.23-15                      IRanges_2.5.40                         
[118] codetools_0.2-14                        MASS_7.3-45                             gtools_3.5.0                           
[121] assertthat_0.1                          chron_2.3-47                            SummarizedExperiment_1.1.24            
[124] rjson_0.2.15                            withr_1.0.1                             mnormt_1.5-4                           
[127] GenomicAlignments_1.7.20                Rsamtools_1.23.8                        multcomp_1.4-4                         
[130] S4Vectors_0.9.44                        mgcv_1.8-12                             parallel_3.3.0                         
[133] grid_3.3.0                              sjPlot_1.9.4                            tidyr_0.4.1                            
[136] minqa_1.2.4                             Biobase_2.31.3                         

Your help is appreciated! Thank you! 

Regards,

Marcel 

bug tcgabiolinks • 616 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Marcel Ramos ♦♦ 410
1

Hi Marcel,

I'm running the same code and it is working. Also, could you please see if the folder "~/Documents/rawdata/" was created?

-------------------------------------------------------------------------------------------------------------------

> prad <- TCGAquery(tumor = "prad", platform = "IlluminaHiSeq_RNASeqV2", level = 3)
> TCGAdownload(prad, "/home/tiagochst/rawdata", type = "bt.exon_quantification")
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:550 files
| Path:/home/tiagochst/rawdata/unc.edu_PRAD.IlluminaHiSeq_RNASeqV2.Level_3.1.14.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |                                                                                                                             |   0%
[1] unc.edu.011453b6-9736-4ea4-8845-bbe4416783d3.1755416.bt.exon_quantification.txt

[2] unc.edu.0120b5b1-d204-429a-aa21-704fd98624ea.1755653.bt.exon_quantification.txt

[3] unc.edu.01234d47-e213-401f-b4fe-f33b15bcec7d.2597947.bt.exon_quantification.txt

  |=                                                                                                                            |   1%
[4] unc.edu.01d4c289-6d85-4119-86f5-bcf3de30d0f7.1753232.bt.exon_quantification.txt

[5] unc.edu.02334a5d-c3a2-4ea6-8e4e-d603a8fbc43c.1760313.bt.exon_quantification.txt

[6] unc.edu.024fc1c9-4502-4293-a555-9bb7e5536f45.2602835.bt.exon_quantification.txt

-------------------------------------------------------------------

What I think it is happening is that TCGA was down for some reason. When you specify the type, it access the TCGA to get the files available, then it filter by type. I believe the files variable received NULL in this case and this messed with the test.

Could you try it again? I'll try to figure a way to verify if TCGA is available or not and alert the user. This is missing in the code.

 

I hope it works.

Best regards,

Tiago

 

ADD REPLYlink written 3.5 years ago by tiagochst150
Answer: Downloading bt.exon_quantification with TCGAbiolinks
0
gravatar for Marcel Ramos
3.5 years ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

Hi Tiago, 

Thank you for your prompt response. Yes, the directory was created.

It seems like the issue has to do with tilde expansion. 

Compare: 

TCGAdownload(prad, "~/Documents/rawdata/", type = "bt.exon_quantification")

TCGAdownload(prad, "/home/mr148/Documents/rawdata/", type = "bt.exon_quantification")

Where the former call fails and the latter works. 

Best regards,

Marcel 

ADD COMMENTlink written 3.5 years ago by Marcel Ramos ♦♦ 410
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