Question: Downloading Thymoma data (THYM)
gravatar for Marcel Ramos
3.5 years ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

Hi there,

I'm trying to download the Thymoma data from TCGAbiolinks::TCGAquery_maf but I am unable to because I get an error:

thym <- TCGAquery_maf(tumor = "thym")

Error in df$Deploy.Status : $ operator is invalid for atomic vectors 

3 subset.default(df, df$Deploy.Status == "Available") 
2 subset(df, df$Deploy.Status == "Available") 
1 TCGAquery_maf(tumor = "thym") 

> sessionInfo()
R Under development (unstable) (2015-11-25 r69695)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

[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=en_US.UTF-8           LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8    

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

other attached packages:
[1] TCGAbiolinks_1.1.24

loaded via a namespace (and not attached):
  [1] circlize_0.3.5                          aroma.light_3.1.1                       selectr_0.2-3                           plyr_1.8.3                            
  [5] igraph_1.0.1                            ConsensusClusterPlus_1.35.0             splines_3.3.0                           BiocParallel_1.5.21                   
  [9] GenomeInfoDb_1.7.6                      ggplot2_2.1.0                           TH.data_1.0-7                           digest_0.6.9                          
[13] foreach_1.4.3                           BiocInstaller_1.21.4                    rsconnect_0.4.2.1                       gdata_2.17.0                          
[17] magrittr_1.5                            memoise_1.0.0                           xlsx_0.5.7                              cluster_2.0.3                         
[21] doParallel_1.0.10                       limma_3.27.14                           ComplexHeatmap_1.9.4                    Biostrings_2.39.12                    
[25] annotate_1.49.1                         matrixStats_0.50.1                      R.utils_2.2.0                           sandwich_2.3-4                        
[29] colorspace_1.2-6                        rvest_0.3.1                             haven_0.2.0                             dplyr_0.4.3                           
[33] RCurl_1.95-4.8                          hexbin_1.27.1                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 graph_1.49.1                          
[37] genefilter_1.53.3                       lme4_1.1-11                             supraHex_1.9.0                          survival_2.38-3                       
[41] zoo_1.7-12                              iterators_1.0.8                         ape_3.4                                 gtable_0.2.0                          
[45] zlibbioc_1.17.1                         CNTools_1.27.0                          XVector_0.11.7                          MatrixModels_0.4-1                    
[49] GetoptLong_0.1.2                        sjmisc_1.6                              car_2.1-2                               Rgraphviz_2.15.0                      
[53] shape_1.4.2                             BiocGenerics_0.17.3                     SparseM_1.7                             scales_0.4.0                          
[57] DESeq_1.23.1                            mvtnorm_1.0-5                           DBI_0.3.1                               GGally_1.0.1                          
[61] edgeR_3.13.5                            Rcpp_0.12.4                             xtable_1.8-2                            matlab_1.0.2                          
[65] preprocessCore_1.33.0                   stats4_3.3.0                            httr_1.1.0                              gplots_3.0.1                          
[69] RColorBrewer_1.1-2                      modeltools_0.2-21                       rJava_0.9-8                             reshape_0.8.5                         
[73] XML_3.98-1.4                            R.methodsS3_1.7.1                       nnet_7.3-12                             reshape2_1.4.1                        
[77] AnnotationDbi_1.33.7                    munsell_0.4.3                           downloader_0.4                          RSQLite_1.0.0                         
[81] devtools_1.10.0                         stringr_1.0.0                           caTools_1.17.1                          dendextend_1.1.8                      
[85] coin_1.1-2                              EDASeq_2.5.1                            nlme_3.1-126                            whisker_0.3-2                         
[89] quantreg_5.21                           R.oo_1.20.0                             xml2_0.1.2                              biomaRt_2.27.2                        
[93] pbkrtest_0.4-6                          curl_0.9.6                              affyio_1.41.0                           geneplotter_1.49.0                    
[97] stringi_1.0-1                           GenomicFeatures_1.23.27                 lattice_0.20-33                         Matrix_1.2-4                          
[101] psych_1.5.8                             nloptr_1.0.4                            effects_3.1-1                           stringdist_0.9.4.1                    
[105] GlobalOptions_0.0.9                     data.table_1.9.6                        cowplot_0.6.1                           bitops_1.0-6                          
[109] dnet_1.0.7                              rtracklayer_1.31.9                      GenomicRanges_1.23.25                   R6_2.1.2                              
[113] latticeExtra_0.6-28                     affy_1.49.0                             hwriter_1.3.2                           ShortRead_1.29.2                      
[117] KernSmooth_2.23-15                      IRanges_2.5.40                          codetools_0.2-14                        MASS_7.3-45                           
[121] gtools_3.5.0                            assertthat_0.1                          xlsxjars_0.6.1                          chron_2.3-47                          
[125] SummarizedExperiment_1.1.22             rjson_0.2.15                            mnormt_1.5-4                            GenomicAlignments_1.7.20              
[129] Rsamtools_1.23.6                        cghMCR_1.29.0                           multcomp_1.4-4                          S4Vectors_0.9.44                      
[133] mgcv_1.8-12                             parallel_3.3.0                          grid_3.3.0                              sjPlot_1.9.4                          
[137] tidyr_0.4.1                             minqa_1.2.4                             Biobase_2.31.3                         

Thank you. 


bug tcgabiolinks • 623 views
ADD COMMENTlink written 3.5 years ago by Marcel Ramos ♦♦ 410

Hi Marcel,

thank you for pointing the bug. It will be fixed in version 1.1.25, otherwise you can download from the github repository.

Best regards,


ADD REPLYlink written 3.5 years ago by tiagochst150
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