cgdsR 下载TCGA数据

TCGA 的数据可以在5个组织机构获取，它们都提供了类似的接口来供用户下载数据。

cgdsR 包是cBioPortal 提供的R包

http://www.cbioportal.org/rmatlab

cgds -- Cancer genomic Data Service

安装 cgdsR

>install.packages("cgdsR", repos="http://cran.us.r-project.org")

使用 cgdsR

library("cgdsr")

# Create CGDS object

mycgds = CGDS("http://www.cbioportal.org/")

# Test the CGDS endpoint URL using a few simple API tests

test(mycgds)

# Get list of cancer studies at server 获取有哪些数据集

getCancerStudies(mycgds)

# Get available case lists (collection of samples) for a given cancer study 获取样本列表

mycancerstudy = getCancerStudies(mycgds)[2,1]

mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]

# Get available genetic profiles

mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[4,1]

# Get data slices for a specified list of genes, genetic profile and case list

getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)

# Get clinical data for the case list

myclinicaldata = getClinicalData(mycgds,mycaselist)

查看帮助信息

help("cgdsr")

help("CGDS")

http://www.360doc.com/content/18/0511/16/42030643_753139769.shtml

https://www.jianshu.com/p/9e3ee12280f5