学学习笔记：利用TCGA Assembler工具下载及处理数据

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")