TCGAquery_subtype: Working with molecular subtypes data.

The Cancer Genome Atlas (TCGA) Research Network has reported integrated genome-wide studies of various diseases. We have added some of the subtypes defined by these report in our package:

These subtypes will be automatically added in the summarizedExperiment object through GDCprepare. But you can also use the TCGAquery_subtype function to retrive this information.

lgg.gbm.subtype <- TCGAquery_subtype(tumor = "lgg")

A subset of the LGG subytpe is shown below:

Session Information

sessionInfo()

## R version 3.5.1 Patched (2018-07-12 r74967)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.7-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.7-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [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] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] TCGAbiolinks_2.8.4          maftools_1.6.15            
##  [3] bigmemory_4.5.33            bindrcpp_0.2.2             
##  [5] png_0.1-7                   DT_0.4                     
##  [7] dplyr_0.7.6                 SummarizedExperiment_1.10.1
##  [9] DelayedArray_0.6.5          BiocParallel_1.14.2        
## [11] matrixStats_0.54.0          Biobase_2.40.0             
## [13] GenomicRanges_1.32.6        GenomeInfoDb_1.16.0        
## [15] IRanges_2.14.11             S4Vectors_0.18.3           
## [17] BiocGenerics_0.26.0        
## 
## loaded via a namespace (and not attached):
##   [1] changepoint_2.2.2           backports_1.1.2            
##   [3] circlize_0.4.4              aroma.light_3.10.0         
##   [5] NMF_0.21.0                  plyr_1.8.4                 
##   [7] selectr_0.4-1               ConsensusClusterPlus_1.44.0
##   [9] lazyeval_0.2.1              splines_3.5.1              
##  [11] crosstalk_1.0.0             gridBase_0.4-7             
##  [13] ggplot2_3.0.0               sva_3.28.0                 
##  [15] digest_0.6.16               foreach_1.4.4              
##  [17] htmltools_0.3.6             magrittr_1.5               
##  [19] memoise_1.1.0               BSgenome_1.48.0            
##  [21] cluster_2.0.7-1             doParallel_1.0.11          
##  [23] limma_3.36.3                ComplexHeatmap_1.18.1      
##  [25] Biostrings_2.48.0           readr_1.1.1                
##  [27] annotate_1.58.0             wordcloud_2.6              
##  [29] R.utils_2.7.0               prettyunits_1.0.2          
##  [31] colorspace_1.3-2            blob_1.1.1                 
##  [33] rvest_0.3.2                 ggrepel_0.8.0              
##  [35] bigmemory.sri_0.1.3         crayon_1.3.4               
##  [37] RCurl_1.95-4.11             jsonlite_1.5               
##  [39] roxygen2_6.1.0              genefilter_1.62.0          
##  [41] bindr_0.1.1                 VariantAnnotation_1.26.1   
##  [43] survival_2.42-6             zoo_1.8-3                  
##  [45] iterators_1.0.10            glue_1.3.0                 
##  [47] survminer_0.4.3             registry_0.5               
##  [49] gtable_0.2.0                zlibbioc_1.26.0            
##  [51] XVector_0.20.0              GetoptLong_0.1.7           
##  [53] shape_1.4.4                 scales_1.0.0               
##  [55] DESeq_1.32.0                rngtools_1.3.1             
##  [57] DBI_1.0.0                   edgeR_3.22.3               
##  [59] bibtex_0.4.2                ggthemes_4.0.1             
##  [61] Rcpp_0.12.18                xtable_1.8-3               
##  [63] progress_1.2.0              cmprsk_2.2-7               
##  [65] mclust_5.4.1                bit_1.1-14                 
##  [67] matlab_1.0.2                km.ci_0.5-2                
##  [69] htmlwidgets_1.2             httr_1.3.1                 
##  [71] RColorBrewer_1.1-2          pkgconfig_2.0.2            
##  [73] XML_3.98-1.16               R.methodsS3_1.7.1          
##  [75] locfit_1.5-9.1              reshape2_1.4.3             
##  [77] later_0.7.4                 labeling_0.3               
##  [79] tidyselect_0.2.4            rlang_0.2.2                
##  [81] AnnotationDbi_1.42.1        munsell_0.5.0              
##  [83] tools_3.5.1                 downloader_0.4             
##  [85] RSQLite_2.1.1               devtools_1.13.6            
##  [87] broom_0.5.0                 evaluate_0.11              
##  [89] stringr_1.3.1               yaml_2.2.0                 
##  [91] knitr_1.20                  bit64_0.9-7                
##  [93] survMisc_0.5.5              purrr_0.2.5                
##  [95] EDASeq_2.14.1               nlme_3.1-137               
##  [97] mime_0.5                    R.oo_1.22.0                
##  [99] xml2_1.2.0                  biomaRt_2.36.1             
## [101] BiocStyle_2.8.2             compiler_3.5.1             
## [103] curl_3.2                    testthat_2.0.0             
## [105] tibble_1.4.2                geneplotter_1.58.0         
## [107] stringi_1.2.4               highr_0.7                  
## [109] GenomicFeatures_1.32.2      lattice_0.20-35            
## [111] Matrix_1.2-14               commonmark_1.5             
## [113] KMsurv_0.1-5                pillar_1.3.0               
## [115] GlobalOptions_0.1.0         cowplot_0.9.3              
## [117] data.table_1.11.4           bitops_1.0-6               
## [119] httpuv_1.4.5                rtracklayer_1.40.6         
## [121] R6_2.2.2                    latticeExtra_0.6-28        
## [123] hwriter_1.3.2               promises_1.0.1             
## [125] ShortRead_1.38.0            gridExtra_2.3              
## [127] codetools_0.2-15            assertthat_0.2.0           
## [129] pkgmaker_0.27               rprojroot_1.3-2            
## [131] rjson_0.2.20                withr_2.1.2                
## [133] GenomicAlignments_1.16.0    Rsamtools_1.32.3           
## [135] GenomeInfoDbData_1.1.0      mgcv_1.8-24                
## [137] hms_0.4.2                   tidyr_0.8.1                
## [139] rmarkdown_1.10              ggpubr_0.1.8               
## [141] shiny_1.1.0