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