Alternatives to TCGAbiolinks todownload the TCGA Data

Question

[gokce.ouz]

Hi All,

library(TCGAbiolinks) is giving errors as gridExtra was renamed so I can not use it to download and analyzing the TCGA data. Except GDC Portal (our IT support having problems to install the data transfer tool, so I can not use it right now) is there any other alternatives to get the TCGA-BRCA data to do differential gene expression analysis.

Thanks,

Gokce

Answer 1

[ivivek_ngs]

Can you show what you are doing and replicate the error so as to make up help you, if a dependency package or module is renamed then it should be also forked into the TCGAbiolonks package if all install.dependancies are made TRUE. If it's a bug then you can always contact their GitHub repo to report it.

Alternative is TCGA2STAT. Take a look at it. I believe you are just downloading the open files and not controlled access data so this package should also work and then you can use your custom lima-voom, edgeR or DESeq2 for your downstream analysis once you have all the meta-data and the count data downloaded for yourself.

[gokce.ouz]

Thanks a lot for your reply. I will check the alternative you suggested. Also I posted the issue at github, but saw that another user also raised it 8 days ago. Hopefully, they will fix the issue soon. The error occurs when I want to use the library. The installations of R packages are done by system admin as we are using R on server therefore I can not comment about all install.dependancies are made TRUE or not.

source("http://bioconductor.org/biocLite.R") 
library(TCGAbiolinks)

Warning: program compiled against libxml 209 using older 207 Error: package or namespace load failed for TCGAbiolinks: object rbind.gtable is not exported by 'namespace:gridExtra'

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

Matrix products: default
BLAS: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRblas.so
LAPACK: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] 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] BiocInstaller_1.26.1

[gokce.ouz]

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

Matrix products: default
BLAS: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRblas.so
LAPACK: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] 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] BiocInstaller_1.26.1

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            selectr_0.3-1              
  [3] rjson_0.2.15                hwriter_1.3.2              
  [5] class_7.3-14                modeltools_0.2-21          
  [7] mclust_5.3                  circlize_0.4.1             
  [9] XVector_0.16.0              GenomicRanges_1.28.5       
 [11] GlobalOptions_0.0.12        ggrepel_0.6.5              
 [13] flexmix_2.3-14              bit64_0.9-7                
 [15] AnnotationDbi_1.38.2        mvtnorm_1.0-6              
 [17] xml2_1.1.1                  codetools_0.2-15           
 [19] splines_3.4.1               R.methodsS3_1.7.1          
 [21] doParallel_1.0.10           DESeq_1.28.0               
 [23] robustbase_0.92-7           geneplotter_1.54.0         
 [25] Rsamtools_1.28.0            annotate_1.54.0            
 [27] cluster_2.0.6               kernlab_0.9-25             
 [29] R.oo_1.21.0                 readr_1.1.1                
 [31] compiler_3.4.1              httr_1.3.1                 
 [33] assertthat_0.2.0            Matrix_1.2-11              
 [35] lazyeval_0.2.0              limma_3.32.6               
 [37] tools_3.4.1                 bindrcpp_0.2               
 [39] gtable_0.2.0                glue_1.1.1                 
 [41] GenomeInfoDbData_0.99.0     dplyr_0.7.3                
 [43] ggthemes_3.4.0              ShortRead_1.34.1           
 [45] Rcpp_0.12.12                Biobase_2.36.2             
 [47] trimcluster_0.1-2           Biostrings_2.44.2          
 [49] rtracklayer_1.36.4          iterators_1.0.8            
 [51] fpc_2.1-10                  stringr_1.2.0              
 [53] XML_3.98-1.9                dendextend_1.5.2           
 [55] edgeR_3.18.1                DEoptimR_1.0-8             
 [57] zlibbioc_1.22.0             MASS_7.3-47                
 [59] scales_0.5.0                aroma.light_3.6.0          
 [61] hms_0.3                     parallel_3.4.1             
 [63] SummarizedExperiment_1.6.3  RColorBrewer_1.1-2         
 [65] ComplexHeatmap_1.14.0       memoise_1.1.0              
 [67] gridExtra_2.3               ggplot2_2.2.1              
 [69] downloader_0.4              biomaRt_2.32.1             
 [71] latticeExtra_0.6-28         stringi_1.1.5              
 [73] RSQLite_2.0                 genefilter_1.58.1          
 [75] S4Vectors_0.14.4            foreach_1.4.3              
 [77] GenomicFeatures_1.28.4      BiocGenerics_0.22.0        
 [79] BiocParallel_1.10.1         shape_1.4.3                
 [81] GenomeInfoDb_1.12.2         rlang_0.1.2                
 [83] pkgconfig_2.0.1             prabclus_2.2-6             
 [85] matrixStats_0.52.2          bitops_1.0-6               
 [87] lattice_0.20-35             bindr_0.1                  
 [89] GenomicAlignments_1.12.2    bit_1.1-12                 
 [91] plyr_1.8.4                  magrittr_1.5               
 [93] R6_2.2.2                    IRanges_2.10.3             
 [95] DelayedArray_0.2.7          DBI_0.7                    
 [97] whisker_0.3-2               survival_2.41-3            
 [99] RCurl_1.95-4.8              nnet_7.3-12                
[101] tibble_1.3.4                EDASeq_2.10.0              
[103] viridis_0.4.0               GetoptLong_0.1.6           
[105] locfit_1.5-9.1              grid_3.4.1                 
[107] data.table_1.10.4           blob_1.1.0                 
[109] ConsensusClusterPlus_1.40.0 digest_0.6.12              
[111] diptest_0.75-7              xtable_1.8-2               
[113] R.utils_2.5.0               stats4_3.4.1               
[115] munsell_0.4.3               viridisLite_0.2.0

[ivivek_ngs]

I just saw in another of your post that a package module function name is changed . It has to be addressed by the group which is using that package having the name of the module hard coded in TCGAbiolinks command. If that function is compatible with new name then remove the concerned package and download the latest version and use it. But I guess you already have an answer of it in the other thread. It's a problem of namespace so yes you will have to see if someone fixes it at the github issue you raised. Else use to TCGA2STAT . This should work. Good luck!

[gokce.ouz]

Hi vchris_ngs,

I checked the TCGA2STAT. As you said it is what I need,thanks a lot! However, I guess the luck is not on my side, because now, I am getting segfault errors which I posted here to ask for help.