環(huán)境設(shè)置
rm(list = ls())
options(stringsAsFactors = F)
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
library(GEOquery)
library(clusterProfiler)
library(org.Hs.eg.db)
dir.create("01_GEOquery版_下載數(shù)據(jù)")
自定義下載GEO的函數(shù)
downGSE <- function(studyID, destdir = destdir) { ##destdir-->之后要存儲數(shù)據(jù)的路徑
library(GEOquery)
eSet <- getGEO(studyID, destdir = destdir, getGPL = T)
exprSet = exprs(eSet[[1]])
pdata = pData(eSet[[1]])
fdata = fData(eSet[[1]])
write.csv(exprSet, paste0(destdir,studyID, "_exprSet.csv"))
write.csv(pdata, paste0(destdir,studyID, "_metadata.csv"))
write.csv(fdata, paste0(destdir,studyID, "_featuredata.csv"))
return(eSet) ##返回下載的元素
}
GSE_ID <- c('GSE33000')
destdir<-c("01_GEOquery版_下載數(shù)據(jù)")
gset<-downGSE(GSE_ID,destdir) ### 輸入你想要的數(shù)據(jù)集和你想儲存數(shù)據(jù)的路徑
