TCGA数据下载R包-RTCGAToolbox说明

安装

# 安装与加载R包
source("https://bioconductor.org/biocLite.R")
biocLite("RTCGAToolbox")
library(RTCGAToolbox)
getFirehoseDatasets() #查看可选的组织类型
 [1] “ACC” “BLCA” “BRCA” “CESC” “CHOL” “COADREAD”
 [7] “COAD” “DLBC” “ESCA” “FPPP” “GBMLGG” “GBM”
 [13] “HNSC” “KICH” “KIPAN” “KIRC” “KIRP” “LAML”
 [19] “LGG” “LIHC” “LUAD” “LUSC” “MESO” “OV”
 [25] “PAAD” “PCPG” “PRAD” “READ” “SARC” “SKCM”
 [31] “STAD” “STES” “TGCT” “THCA” “THYM” “UCEC”
 [37] “UCS” “UVM”

查看数据更新时间

getFirehoseRunningDates()

数据下载

设置数据存储路径

stewed('/your/pwd')

选择要下载的数据及具体的数据类目

BLCAdata <- getFirehoseData(dataset = "BLCA",runDate = "20160128",gistic2_Date = "20160128",RNAseq_Gene = TRUE,Clinic = TRUE,Mutation = TRUE)

获取数据中的临床数据

BLCAClinical = getData(BLCAdata,"Clinical")