下载包的作者提供的下载地址:https://github.com/compgenome365/TCGA-Assembler-2
文献引用:TCGA assembler 2: software pipeline for retrieval and progressing of TCGA/CPTAC data
参考操作说明:https://cloud.tencent.com/developer/article/1481868
工作环境准备
安装包
getwd()
source("https://bioconductor.org/biocLite.R")
biocLite("httr")
biocLite("RCurl")
biocLite("stringr")
biocLite("HGNChelper")
biocLite("rjson")
library(httr)
library(bitops)
library(RCurl)
library(stringr)
library(HGNChelper)
library(rjson)
library(digest)
##download clinical data
#https://tcga-data.nci.nih.gov/docs/publications/tcga/
#查看癌症缩写
source("Module_A.R")
source("Module_B.R")
利用Model_A下载数据
以COAD的CPTAC数据为例:
filename_coad_CPTAC <-DownloadCPTACData(cancerType="COAD",
assayPlatform = "proteome_iTRAQ",
saveFolderName = "./ManualExampleData/RawData.TCGA-Assembler")
利用Model_B处理数据
source("Module_B.R")
CPTACData <-
ProcessCPTACData(inputFilePath = filename_read_CPTAC[1],
outputFileName = "COAD_iTRAQData",
outputFileFolder = "./ManualExampleData/ProcessedData.TCGA-Assembler")