TCGAbiolinks下载TCGA数据

#以下为安装TCGAbiolinks的R包
#1）第一种
 if (!requireNamespace("BiocManager", quietly=TRUE))
   install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")
#2）第二种
#可以先下载到本地安装比较快
#Tools  >  install.packages
#3) 第三种
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
#################################
# TCGA-12-4567-01-blah-blah --> 这是Normal
# TCGA-12-4567-11-blah-blah --> 这是tumor
# 注意黑体的部分。01-09是tumor；10-19是Normal；20-29是Control

####加载程序包
library(TCGAbiolinks)
library(dplyr)
library(DT)
library(SummarizedExperiment)
#################################

#下面填入要下载的癌症种类
request_cancer=c("PRAD","BLCA","KICH","KIRC","KIRP")
for (i in request_cancer) {
  cancer_type=paste("TCGA",i,sep="-")
  print(cancer_type)
  #下载临床数据
  clinical <- GDCquery_clinic(project = cancer_type, type = "clinical")
  write.csv(clinical,file = paste(cancer_type,"clinical.csv",sep = "-"))
  
  #下载rna-seq的counts数据
  query <- GDCquery(project = cancer_type, 
                    data.category = "Transcriptome Profiling", 
                    data.type = "Gene Expression Quantification", 
                    workflow.type = "HTSeq - Counts")
  
  GDCdownload(query, method = "api", files.per.chunk = 100)
  expdat <- GDCprepare(query = query)
  count_matrix=assay(expdat)
  write.csv(count_matrix,file = paste(cancer_type,"Counts.csv",sep = "-"))
  
  #下载miRNA数据
  query <- GDCquery(project = cancer_type, 
                    data.category = "Transcriptome Profiling", 
                    data.type = "miRNA Expression Quantification", 
                    workflow.type = "BCGSC miRNA Profiling")
  
  GDCdownload(query, method = "api", files.per.chunk = 50)
  expdat <- GDCprepare(query = query)
  count_matrix=assay(expdat)
  write.csv(count_matrix,file = paste(cancer_type,"miRNA.csv",sep = "-"))
  
  #下载Copy Number Variation数据
  query <- GDCquery(project = cancer_type, 
                    data.category = "Copy Number Variation", 
                    data.type = "Copy Number Segment")
  
  GDCdownload(query, method = "api", files.per.chunk = 50)
  expdat <- GDCprepare(query = query)
  count_matrix=assay(expdat)
  write.csv(count_matrix,file = paste(cancer_type,"Copy-Number-Variation.csv",sep = "-"))
  
  #下载甲基化数据
  query.met <- GDCquery(project =cancer_type,
                        legacy = TRUE,
                        data.category = "DNA methylation")
  GDCdownload(query.met, method = "api", files.per.chunk = 300)
  expdat <- GDCprepare(query = query)
  count_matrix=assay(expdat)
  write.csv(count_matrix,file = paste(cancer_type,"methylation.csv",sep = "-"))
}

参考