PanCancerAtlas_subtypes: Curated molecular subtypes.

Data and description retrieved from synapse (https://www.synapse.org/#!Synapse:syn8402849)

Synapse has published a single file with all available molecular subtypes that have been described by TCGA (all tumor types and all molecular platforms), which can be accessed using the PanCancerAtlas_subtypes function as below:

subtypes <- PanCancerAtlas_subtypes()
DT::datatable(
    data = subtypes,
    filter = 'top',
    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
    rownames = FALSE
)

The columns “Subtype_Selected” was selected as most prominent subtype classification (from the other columns)

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 retrieve this information.

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

## lgg subtype information from:doi:10.1016/j.cell.2015.12.028

A subset of the LGG subytpe is shown below:

Session Information

sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## 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       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] grid      stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] maftools_2.23.0             jpeg_0.1-10                
##  [3] png_0.1-8                   DT_0.33                    
##  [5] dplyr_1.1.4                 SummarizedExperiment_1.37.0
##  [7] Biobase_2.67.0              GenomicRanges_1.59.1       
##  [9] GenomeInfoDb_1.43.1         IRanges_2.41.1             
## [11] S4Vectors_0.45.2            BiocGenerics_0.53.3        
## [13] generics_0.1.3              MatrixGenerics_1.19.0      
## [15] matrixStats_1.4.1           TCGAbiolinks_2.35.0        
## [17] testthat_3.2.1.1           
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          sys_3.4.3                  
##   [3] rstudioapi_0.17.1           jsonlite_1.8.9             
##   [5] magrittr_2.0.3              GenomicFeatures_1.59.1     
##   [7] rmarkdown_2.29              BiocIO_1.17.0              
##   [9] fs_1.6.5                    zlibbioc_1.52.0            
##  [11] vctrs_0.6.5                 Rsamtools_2.23.0           
##  [13] memoise_2.0.1               RCurl_1.98-1.16            
##  [15] htmltools_0.5.8.1           S4Arrays_1.7.1             
##  [17] usethis_3.0.0               progress_1.2.3             
##  [19] curl_6.0.1                  SparseArray_1.7.2          
##  [21] sass_0.4.9                  bslib_0.8.0                
##  [23] htmlwidgets_1.6.4           desc_1.4.3                 
##  [25] plyr_1.8.9                  httr2_1.0.6                
##  [27] cachem_1.1.0                GenomicAlignments_1.43.0   
##  [29] buildtools_1.0.0            mime_0.12                  
##  [31] lifecycle_1.0.4             pkgconfig_2.0.3            
##  [33] Matrix_1.7-1                R6_2.5.1                   
##  [35] fastmap_1.2.0               GenomeInfoDbData_1.2.13    
##  [37] shiny_1.9.1                 digest_0.6.37              
##  [39] colorspace_2.1-1            ShortRead_1.65.0           
##  [41] AnnotationDbi_1.69.0        rprojroot_2.0.4            
##  [43] pkgload_1.4.0               crosstalk_1.2.1            
##  [45] RSQLite_2.3.8               hwriter_1.3.2.1            
##  [47] filelock_1.0.3              fansi_1.0.6                
##  [49] httr_1.4.7                  abind_1.4-8                
##  [51] compiler_4.4.2              remotes_2.5.0              
##  [53] bit64_4.5.2                 withr_3.0.2                
##  [55] downloader_0.4              BiocParallel_1.41.0        
##  [57] DBI_1.2.3                   pkgbuild_1.4.5             
##  [59] R.utils_2.12.3              biomaRt_2.63.0             
##  [61] rappdirs_0.3.3              DelayedArray_0.33.2        
##  [63] sessioninfo_1.2.2           rjson_0.2.23               
##  [65] DNAcopy_1.81.0              tools_4.4.2                
##  [67] httpuv_1.6.15               R.oo_1.27.0                
##  [69] glue_1.8.0                  restfulr_0.0.15            
##  [71] promises_1.3.0              gtable_0.3.6               
##  [73] tzdb_0.4.0                  R.methodsS3_1.8.2          
##  [75] tidyr_1.3.1                 data.table_1.16.2          
##  [77] hms_1.1.3                   xml2_1.3.6                 
##  [79] utf8_1.2.4                  XVector_0.47.0             
##  [81] pillar_1.9.0                stringr_1.5.1              
##  [83] vroom_1.6.5                 later_1.3.2                
##  [85] splines_4.4.2               BiocFileCache_2.15.0       
##  [87] lattice_0.22-6              deldir_2.0-4               
##  [89] rtracklayer_1.67.0          aroma.light_3.37.0         
##  [91] survival_3.7-0              bit_4.5.0                  
##  [93] tidyselect_1.2.1            maketools_1.3.1            
##  [95] Biostrings_2.75.1           miniUI_0.1.1.1             
##  [97] knitr_1.49                  xfun_0.49                  
##  [99] devtools_2.4.5              brio_1.1.5                 
## [101] stringi_1.8.4               UCSC.utils_1.3.0           
## [103] yaml_2.3.10                 codetools_0.2-20           
## [105] TCGAbiolinksGUI.data_1.26.0 evaluate_1.0.1             
## [107] interp_1.1-6                EDASeq_2.41.0              
## [109] tibble_3.2.1                BiocManager_1.30.25        
## [111] cli_3.6.3                   xtable_1.8-4               
## [113] munsell_0.5.1               jquerylib_0.1.4            
## [115] Rcpp_1.0.13-1               dbplyr_2.5.0               
## [117] XML_3.99-0.17               parallel_4.4.2             
## [119] ellipsis_0.3.2              ggplot2_3.5.1              
## [121] readr_2.1.5                 blob_1.2.4                 
## [123] prettyunits_1.2.0           latticeExtra_0.6-30        
## [125] profvis_0.4.0               urlchecker_1.0.1           
## [127] bitops_1.0-9                pwalign_1.3.0              
## [129] scales_1.3.0                purrr_1.0.2                
## [131] crayon_1.5.3                BiocStyle_2.35.0           
## [133] rlang_1.1.4                 KEGGREST_1.47.0            
## [135] rvest_1.0.4