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(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 retrive this information.

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

A subset of the LGG subytpe is shown below:

Session Information

sessionInfo()

## R version 3.5.3 (2019-03-11)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.6 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.8-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_2.10.5         maftools_1.8.0             
##  [3] bigmemory_4.5.33            png_0.1-7                  
##  [5] DT_0.5                      dplyr_0.8.0.1              
##  [7] SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
##  [9] BiocParallel_1.16.6         matrixStats_0.54.0         
## [11] Biobase_2.42.0              GenomicRanges_1.34.0       
## [13] GenomeInfoDb_1.18.2         IRanges_2.16.0             
## [15] S4Vectors_0.20.1            BiocGenerics_0.28.0        
## [17] testthat_2.0.1             
## 
## loaded via a namespace (and not attached):
##   [1] R.utils_2.8.0                 tidyselect_0.2.5             
##   [3] RSQLite_2.1.1                 AnnotationDbi_1.44.0         
##   [5] htmlwidgets_1.3               devtools_2.0.1               
##   [7] DESeq_1.34.1                  munsell_0.5.0                
##   [9] codetools_0.2-16              preprocessCore_1.44.0        
##  [11] withr_2.1.2                   colorspace_1.4-1             
##  [13] highr_0.7                     knitr_1.22                   
##  [15] rstudioapi_0.10               NMF_0.21.0                   
##  [17] labeling_0.3                  GenomeInfoDbData_1.2.0       
##  [19] hwriter_1.3.2                 KMsurv_0.1-5                 
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##  [27] randomForest_4.6-14           EDASeq_2.16.3                
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##  [49] selectr_0.4-1                 broom_0.5.1                  
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## [103] geneplotter_1.60.0            DBI_1.0.0                    
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## [107] ComplexHeatmap_1.20.0         BiocStyle_2.10.0             
## [109] ShortRead_1.40.0              Matrix_1.2-16                
## [111] readr_1.3.1                   cli_1.1.0                    
## [113] R.methodsS3_1.7.1             bigmemory.sri_0.1.3          
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## [139] rjson_0.2.20                  nlme_3.1-137                 
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## [153] iterators_1.0.10              bit_1.1-14                   
## [155] stringi_1.4.3                 blob_1.1.1                   
## [157] AnnotationHub_2.14.5          latticeExtra_0.6-28          
## [159] memoise_1.1.0