之前一直在用RTCGA包下载数据,看着永不更新的数据,心里总觉得怪怪的,于是下定决心重新学习一个好用的包——TCGAbiolinks。这个包调用GDC的API,应该是最新的数据。
主要参考:TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
# if (!requireNamespace("BiocManager", quietly=TRUE))# install.packages("BiocManager")# BiocManager::install("TCGAbiolinks") 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 = "-"))}
常用的一些数据基本都下下来了,放在当前目录下。
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