Question: Downloading Thymoma data (THYM)
0
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 

Traceback: 
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

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=en_US.UTF-8           LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8    
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=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. 

Marcel 

bug tcgabiolinks • 623 views
ADD COMMENTlink written 3.5 years ago by Marcel Ramos ♦♦ 410
1

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. 

https://github.com/BioinformaticsFMRP/TCGAbiolinks/

Best regards,

Tiago

ADD REPLYlink written 3.5 years ago by tiagochst150
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