TCGA 数据下载 —— TCGAbiolinks 简单使用

前言

前面我们曾介绍过 TCGAbiolinks 的使用，但是由于 TCGA 的改版，该包也做出了相应的更新，所以我再重新介绍一下新版 TCGAbiolinks 的使用。

TCGAbiolinks 是一个利用 GDC API 接口来查询、下载和分析 TCGA 数据库的数据的 R 包

TCGAbiolinks 包的功能主要可以分为三大块：

• 数据查询和下载
• 数据的常规分析
• 可视化

该包可以从 Bioconductor 上安装稳定版本

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")

或者从 GitHub 上安装开发版本

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

导入包

library(TCGAbiolinks)  # version 2.30.4

数据查询

TCGAbiolinks 提供了一些函数用于查询和下载 GDC 中的数据，包括：

• Harmonized：这部分数据都比较新，使用的是 GRCh38 (hg38) 基因组版本，使用的是 GDC pipeline 来处理数据
• Legacy：这部分的数据应该是较早之前测的，使用的是 GRCh37 (hg19) 基因组版本

使用 GDCquery 函数来查询 GDC 的数据，该函数的参数为：

GDCquery(
  project,
  data.category,
  data.type,
  workflow.type,
  access,
  platform,
  barcode,
  data.format,
  experimental.strategy,
  sample.type
)

• project：该参数的取值非常多，可以使用如下命令来查询所有可用的项目

> TCGAbiolinks:::getGDCprojects()$project_id
[1] "HCMI-CMDC"                 "TCGA-BRCA"                 "TARGET-ALL-P3"            
 [4] "EXCEPTIONAL_RESPONDERS-ER" "CGCI-HTMCP-LC"             "CPTAC-2"                  
 [7] "CMI-MBC"                   "TARGET-ALL-P2"             "OHSU-CNL"                 
[10] "TARGET-ALL-P1"             "MMRF-COMMPASS"             "ORGANOID-PANCREATIC"      
[13] "NCICCR-DLBCL"              "TCGA-SARC"                 "TCGA-ACC"                 
[16] "WCDT-MCRPC"                "TCGA-UCEC"                 "MP2PRT-ALL"               
[19] "TCGA-KIRC"                 "CGCI-HTMCP-CC"             "CMI-ASC"                  
[22] "CGCI-HTMCP-DLBCL"          "BEATAML1.0-CRENOLANIB"     "CDDP_EAGLE-1"             
[25] "APOLLO-LUAD"               "CMI-MPC"                   "FM-AD"                    
[28] "MATCH-Z1D"                 "MATCH-Y"                   "MATCH-N"                  
[31] "MATCH-Q"                   "MP2PRT-WT"                 "TCGA-LAML"                
[34] "VAREPOP-APOLLO"            "TCGA-SKCM"                 "TRIO-CRU"                 
[37] "TCGA-PAAD"                 "TCGA-TGCT"                 "TCGA-CESC"                
[40] "TCGA-ESCA"                 "TCGA-THCA"                 "TCGA-LIHC"                
[43] "TCGA-PRAD"                 "TCGA-READ"                 "MATCH-I"                  
[46] "MATCH-W"                   "MATCH-B"                   "MATCH-H"                  
[49] "TCGA-OV"                   "TCGA-UVM"                  "MATCH-Z1A"                
[52] "MATCH-U"                   "BEATAML1.0-COHORT"         "TCGA-BLCA"                
[55] "CGCI-BLGSP"                "CTSP-DLBCL1"               "MATCH-S1"                 
[58] "MATCH-R"                   "MATCH-Z1I"                 "CPTAC-3"                  
[61] "TCGA-CHOL"                 "TCGA-GBM"                  "MATCH-S2"                 
[64] "TCGA-UCS"                  "TCGA-PCPG"                 "TCGA-MESO"                
[67] "TARGET-CCSK"               "TARGET-WT"                 "TARGET-RT"                
[70] "TCGA-DLBC"                 "TARGET-OS"                 "TCGA-COAD"                
[73] "REBC-THYR"                 "TCGA-STAD"                 "TCGA-KIRP"                
[76] "TCGA-THYM"                 "TCGA-KICH"                 "TCGA-LGG"                 
[79] "TARGET-AML"                "TCGA-LUSC"                 "TCGA-LUAD"                
[82] "TCGA-HNSC"                 "TARGET-NBL"

• data.category：可以使用如下方式来查询 TCGA-BRCA 项目的可用的分类数据

> TCGAbiolinks:::getProjectSummary("TCGA-BRCA")
$file_count
[1] 61173

$data_categories
   file_count case_count                data_category
1       17337       1098  Simple Nucleotide Variation
2        9281       1098             Sequencing Reads
3        5316       1098                  Biospecimen
4        2288       1098                     Clinical
5       12292       1098        Copy Number Variation
6        4876       1097      Transcriptome Profiling
7        3714       1097              DNA Methylation
8         919        881           Proteome Profiling
9         226        101 Somatic Structural Variation
10       4924       1095         Structural Variation

$case_count
[1] 1098

$file_size
[1] 6.245362e+14

新版本只能获取 harmonized 类型的数据，主要包含 7 个分类：

- Bio