TCGAbiolinks：分子亚型

在运行程序前，我们需要导入必要的包：

library(TCGAbiolinks)

library(SummarizedExperiment)

TCGAbiolinks从TCGA样本中检索分子亚型信息。函数PanCancerAtlas_subtypes和TCGAquery_subtype可用于获取分子亚型的信息表。

分子亚型实际上指的是测序的数据亚型，比如mRNA、miRNA、DNA甲基化等

虽然PanCancerAtlas_subtypes函数可以从synapse中获得精准的分子亚型表（可能具有最新的分子亚型），但TCGAquery_subtype函数能从TCGA标记的文章中获得完整的分子亚型信息，并带有样本信息。

1. PanCancerAtlas_subtypes：精准的分子亚型。

从synapse中检索数据及其相应的描述可以参考：https://www.synapse.org/#!Synapse:syn8402849

Synapse目前发布了一个文件，其中包含TCGA中所有可用分子亚型，包括所有肿瘤类型和所有分子平台（即测序平台））。我们可以使用PanCancerAtlas_subtypes函数获取信息：

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

只显示了一部分数据

选择“Subtype_Selected”列作为最突出的亚型分类（来自其他列）

2. TCGAquery_subtype：使用分子亚型数据。

癌症基因组图谱（TCGA）研究网络报告了各种疾病的综合全基因组研究。我们在包中添加了这些报告定义的一些分子亚型：

这些分子亚型将通过GDCprepare自动添加到summaExperiment对象中。但您也可以TCGAquery_subtype函数来检索此信息。

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

LGG亚型的子集如下所示：

3. 版本信息

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                 
##  [21] bit64_0.9-7                   rprojroot_1.3-2              
##  [23] downloader_0.4                generics_0.0.2               
##  [25] xfun_0.5                      ggthemes_4.1.0               
##  [27] randomForest_4.6-14           EDASeq_2.16.3                
##  [29] R6_2.4.0                      doParallel_1.0.14            
##  [31] locfit_1.5-9.1                bitops_1.0-6                 
##  [33] assertthat_0.2.0              promises_1.0.1               
##  [35] scales_1.0.0                  gtable_0.2.0                 
##  [37] sva_3.30.1                    processx_3.3.0               
##  [39] wheatmap_0.1.0                sesameData_1.0.0             
##  [41] rlang_0.3.1                   genefilter_1.64.0            
##  [43] cmprsk_2.2-7                  GlobalOptions_0.1.0          
##  [45] splines_3.5.3                 rtracklayer_1.42.2           
##  [47] lazyeval_0.2.2                wordcloud_2.6                
##  [49] selectr_0.4-1                 broom_0.5.1                  
##  [51] reshape2_1.4.3                BiocManager_1.30.4           
##  [53] yaml_2.2.0                    GenomicFeatures_1.34.6       
##  [55] crosstalk_1.0.0               backports_1.1.3              
##  [57] httpuv_1.5.0                  tools_3.5.3                  
##  [59] usethis_1.4.0                 gridBase_0.4-7               
##  [61] ggplot2_3.1.0                 RColorBrewer_1.1-2           
##  [63] DNAcopy_1.56.0                sessioninfo_1.1.1            
##  [65] Rcpp_1.0.1                    plyr_1.8.4                   
##  [67] progress_1.2.0                zlibbioc_1.28.0              
##  [69] purrr_0.3.2                   RCurl_1.95-4.12              
##  [71] ps_1.3.0                      prettyunits_1.0.2            
##  [73] ggpubr_0.2                    GetoptLong_0.1.7             
##  [75] cowplot_0.9.4                 zoo_1.8-4                    
##  [77] ggrepel_0.8.0                 cluster_2.0.7-1              
##  [79] fs_1.2.7                      magrittr_1.5                 
##  [81] data.table_1.12.0             circlize_0.4.5               
##  [83] survminer_0.4.3               pkgload_1.0.2                
##  [85] aroma.light_3.12.0            hms_0.4.2                    
##  [87] mime_0.6                      evaluate_0.13                
##  [89] xtable_1.8-3                  XML_3.98-1.19                
##  [91] mclust_5.4.3                  gridExtra_2.3                
##  [93] shape_1.4.4                   compiler_3.5.3               
##  [95] biomaRt_2.38.0                tibble_2.1.1                 
##  [97] crayon_1.3.4                  R.oo_1.22.0                  
##  [99] htmltools_0.3.6               mgcv_1.8-27                  
## [101] later_0.8.0                   tidyr_0.8.3                  
## [103] geneplotter_1.60.0            DBI_1.0.0                    
## [105] ExperimentHub_1.8.0           matlab_1.0.2                 
## [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          
## [115] pkgconfig_2.0.2               km.ci_0.5-2                  
## [117] sesame_1.0.0                  registry_0.5-1               
## [119] GenomicAlignments_1.18.1      xml2_1.2.0                   
## [121] foreach_1.4.4                 annotate_1.60.1              
## [123] rngtools_1.3.1                pkgmaker_0.27                
## [125] XVector_0.22.0                bibtex_0.4.2                 
## [127] rvest_0.3.2                   stringr_1.4.0                
## [129] callr_3.2.0                   digest_0.6.18                
## [131] ConsensusClusterPlus_1.46.0   Biostrings_2.50.2            
## [133] rmarkdown_1.12                survMisc_0.5.5               
## [135] edgeR_3.24.3                  curl_3.3                     
## [137] shiny_1.2.0                   Rsamtools_1.34.1             
## [139] rjson_0.2.20                  nlme_3.1-137                 
## [141] jsonlite_1.6                  BSgenome_1.50.0              
## [143] desc_1.2.0                    limma_3.38.3                 
## [145] pillar_1.3.1                  lattice_0.20-38              
## [147] httr_1.4.0                    pkgbuild_1.0.2               
## [149] survival_2.43-3               interactiveDisplayBase_1.20.0
## [151] glue_1.3.1                    remotes_2.0.2                
## [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