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 3.4.3 (2017-11-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.6-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.6-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_2.6.12        maftools_1.4.15           
##  [3] bigmemory_4.5.33           bindrcpp_0.2              
##  [5] png_0.1-7                  DT_0.4                    
##  [7] dplyr_0.7.4                SummarizedExperiment_1.8.1
##  [9] DelayedArray_0.4.1         matrixStats_0.53.0        
## [11] Biobase_2.38.0             GenomicRanges_1.30.1      
## [13] GenomeInfoDb_1.14.0        IRanges_2.12.0            
## [15] S4Vectors_0.16.0           BiocGenerics_0.24.0       
## 
## loaded via a namespace (and not attached):
##   [1] changepoint_2.2.2           backports_1.1.2            
##   [3] circlize_0.4.3              aroma.light_3.8.0          
##   [5] NMF_0.20.6                  plyr_1.8.4                 
##   [7] selectr_0.3-1               ConsensusClusterPlus_1.42.0
##   [9] lazyeval_0.2.1              splines_3.4.3              
##  [11] crosstalk_1.0.0             BiocParallel_1.12.0        
##  [13] gridBase_0.4-7              ggplot2_2.2.1              
##  [15] sva_3.26.0                  digest_0.6.15              
##  [17] foreach_1.4.4               htmltools_0.3.6            
##  [19] magrittr_1.5                memoise_1.1.0              
##  [21] BSgenome_1.46.0             cluster_2.0.6              
##  [23] doParallel_1.0.11           limma_3.34.7               
##  [25] ComplexHeatmap_1.17.1       Biostrings_2.46.0          
##  [27] readr_1.1.1                 annotate_1.56.1            
##  [29] wordcloud_2.5               R.utils_2.6.0              
##  [31] prettyunits_1.0.2           colorspace_1.3-2           
##  [33] blob_1.1.0                  rvest_0.3.2                
##  [35] ggrepel_0.7.0               bigmemory.sri_0.1.3        
##  [37] RCurl_1.95-4.10             jsonlite_1.5               
##  [39] roxygen2_6.0.1              genefilter_1.60.0          
##  [41] bindr_0.1                   VariantAnnotation_1.24.5   
##  [43] survival_2.41-3             zoo_1.8-1                  
##  [45] iterators_1.0.9             glue_1.2.0                 
##  [47] survminer_0.4.2             registry_0.5               
##  [49] gtable_0.2.0                zlibbioc_1.24.0            
##  [51] XVector_0.18.0              GetoptLong_0.1.6           
##  [53] shape_1.4.3                 scales_0.5.0               
##  [55] DESeq_1.30.0                rngtools_1.2.4             
##  [57] DBI_0.7                     edgeR_3.20.8               
##  [59] ggthemes_3.4.0              Rcpp_0.12.15               
##  [61] xtable_1.8-2                progress_1.1.2             
##  [63] cmprsk_2.2-7                mclust_5.4                 
##  [65] foreign_0.8-69              bit_1.1-12                 
##  [67] matlab_1.0.2                km.ci_0.5-2                
##  [69] htmlwidgets_1.0             httr_1.3.1                 
##  [71] RColorBrewer_1.1-2          pkgconfig_2.0.1            
##  [73] XML_3.98-1.9                R.methodsS3_1.7.1          
##  [75] locfit_1.5-9.1              labeling_0.3               
##  [77] rlang_0.1.6                 reshape2_1.4.3             
##  [79] AnnotationDbi_1.40.0        munsell_0.4.3              
##  [81] tools_3.4.3                 downloader_0.4             
##  [83] RSQLite_2.0                 devtools_1.13.4            
##  [85] broom_0.4.3                 evaluate_0.10.1            
##  [87] stringr_1.2.0               yaml_2.1.16                
##  [89] knitr_1.19                  bit64_0.9-7                
##  [91] survMisc_0.5.4              purrr_0.2.4                
##  [93] EDASeq_2.12.0               nlme_3.1-131               
##  [95] mime_0.5                    slam_0.1-42                
##  [97] R.oo_1.21.0                 xml2_1.2.0                 
##  [99] biomaRt_2.34.2              BiocStyle_2.6.1            
## [101] compiler_3.4.3              curl_3.1                   
## [103] testthat_2.0.0              tibble_1.4.2               
## [105] geneplotter_1.56.0          stringi_1.1.6              
## [107] highr_0.6                   GenomicFeatures_1.30.3     
## [109] lattice_0.20-35             Matrix_1.2-12              
## [111] commonmark_1.4              psych_1.7.8                
## [113] KMsurv_0.1-5                pillar_1.1.0               
## [115] GlobalOptions_0.0.12        cowplot_0.9.2              
## [117] data.table_1.10.4-3         bitops_1.0-6               
## [119] httpuv_1.3.5                rtracklayer_1.38.3         
## [121] R6_2.2.2                    latticeExtra_0.6-28        
## [123] hwriter_1.3.2               RMySQL_0.10.13             
## [125] ShortRead_1.36.0            gridExtra_2.3              
## [127] codetools_0.2-15            assertthat_0.2.0           
## [129] pkgmaker_0.22               rprojroot_1.3-2            
## [131] rjson_0.2.15                withr_2.1.1                
## [133] GenomicAlignments_1.14.1    Rsamtools_1.30.0           
## [135] mnormt_1.5-5                GenomeInfoDbData_1.0.0     
## [137] mgcv_1.8-23                 hms_0.4.1                  
## [139] tidyr_0.8.0                 rmarkdown_1.8              
## [141] ggpubr_0.1.6                shiny_1.0.5