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 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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_2.27.0             jpeg_0.1-11                
##  [3] png_0.1-8                   DT_0.34.0                  
##  [5] dplyr_1.1.4                 SummarizedExperiment_1.41.0
##  [7] Biobase_2.71.0              GenomicRanges_1.63.1       
##  [9] Seqinfo_1.1.0               IRanges_2.45.0             
## [11] S4Vectors_0.49.0            BiocGenerics_0.57.0        
## [13] generics_0.1.4              MatrixGenerics_1.23.0      
## [15] matrixStats_1.5.0           TCGAbiolinks_2.39.0        
## [17] testthat_3.3.1             
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          sys_3.4.3                  
##   [3] rstudioapi_0.17.1           jsonlite_2.0.0             
##   [5] magrittr_2.0.4              GenomicFeatures_1.63.1     
##   [7] farver_2.1.2                rmarkdown_2.30             
##   [9] fs_1.6.6                    BiocIO_1.21.0              
##  [11] vctrs_0.6.5                 memoise_2.0.1              
##  [13] Rsamtools_2.27.0            RCurl_1.98-1.17            
##  [15] htmltools_0.5.9             S4Arrays_1.11.1            
##  [17] usethis_3.2.1               progress_1.2.3             
##  [19] curl_7.0.0                  SparseArray_1.11.9         
##  [21] sass_0.4.10                 bslib_0.9.0                
##  [23] htmlwidgets_1.6.4           desc_1.4.3                 
##  [25] plyr_1.8.9                  httr2_1.2.2                
##  [27] cachem_1.1.0                GenomicAlignments_1.47.0   
##  [29] buildtools_1.0.0            lifecycle_1.0.4            
##  [31] pkgconfig_2.0.3             Matrix_1.7-4               
##  [33] R6_2.6.1                    fastmap_1.2.0              
##  [35] digest_0.6.39               ShortRead_1.69.2           
##  [37] AnnotationDbi_1.73.0        rprojroot_2.1.1            
##  [39] pkgload_1.4.1               crosstalk_1.2.2            
##  [41] RSQLite_2.4.5               hwriter_1.3.2.1            
##  [43] filelock_1.0.3              httr_1.4.7                 
##  [45] abind_1.4-8                 compiler_4.5.2             
##  [47] remotes_2.5.0               bit64_4.6.0-1              
##  [49] withr_3.0.2                 downloader_0.4.1           
##  [51] S7_0.2.1                    BiocParallel_1.45.0        
##  [53] DBI_1.2.3                   pkgbuild_1.4.8             
##  [55] R.utils_2.13.0              biomaRt_2.67.0             
##  [57] rappdirs_0.3.3              DelayedArray_0.37.0        
##  [59] sessioninfo_1.2.3           rjson_0.2.23               
##  [61] DNAcopy_1.85.0              tools_4.5.2                
##  [63] otel_0.2.0                  R.oo_1.27.1                
##  [65] glue_1.8.0                  restfulr_0.0.16            
##  [67] gtable_0.3.6                tzdb_0.5.0                 
##  [69] R.methodsS3_1.8.2           tidyr_1.3.1                
##  [71] data.table_1.17.8           hms_1.1.4                  
##  [73] xml2_1.5.1                  XVector_0.51.0             
##  [75] pillar_1.11.1               stringr_1.6.0              
##  [77] vroom_1.6.7                 splines_4.5.2              
##  [79] BiocFileCache_3.1.0         lattice_0.22-7             
##  [81] deldir_2.0-4                aroma.light_3.41.0         
##  [83] survival_3.8-3              rtracklayer_1.71.2         
##  [85] bit_4.6.0                   tidyselect_1.2.1           
##  [87] maketools_1.3.2             Biostrings_2.79.2          
##  [89] knitr_1.50                  xfun_0.54                  
##  [91] devtools_2.4.6              brio_1.1.5                 
##  [93] stringi_1.8.7               yaml_2.3.12                
##  [95] cigarillo_1.1.0             TCGAbiolinksGUI.data_1.31.0
##  [97] evaluate_1.0.5              codetools_0.2-20           
##  [99] interp_1.1-6                tibble_3.3.0               
## [101] EDASeq_2.45.0               BiocManager_1.30.27        
## [103] cli_3.6.5                   jquerylib_0.1.4            
## [105] Rcpp_1.1.0.8                dbplyr_2.5.1               
## [107] XML_3.99-0.20               parallel_4.5.2             
## [109] ellipsis_0.3.2              ggplot2_4.0.1              
## [111] readr_2.1.6                 blob_1.2.4                 
## [113] prettyunits_1.2.0           latticeExtra_0.6-31        
## [115] bitops_1.0-9                pwalign_1.7.0              
## [117] scales_1.4.0                purrr_1.2.0                
## [119] crayon_1.5.3                BiocStyle_2.39.0           
## [121] rlang_1.1.6                 KEGGREST_1.51.1            
## [123] rvest_1.0.5