R/downGSE.R

In jmzeng1314/humanid: gene id annotation

#' download the data from GEO database
#'
#' Given a GSE study ID, just like GSE1009, this function will download the eSet object and write the expression matrix and phenotype information.
#' https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1009
#' @param studyID A standard study ID in GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1009
#' @param destdir where to store the files just download.
#' @return A expresstionSet,S4 object in R, which contain: assayData,phenoData,featureData
#' @export
#' @keywords downGSE
#' @examples
#' #' downGSE('GSE1009')


downGSE <- function(studyID = "GSE1009", destdir = ".") {
    
    library(GEOquery)
    eSet <- getGEO(studyID, destdir = destdir, getGPL = F)
    
    exprSet = exprs(eSet[[1]])
    pdata = pData(eSet[[1]])
    
    write.csv(exprSet, paste0(studyID, "_exprSet.csv"))
    write.csv(pdata, paste0(studyID, "_metadata.csv"))
    return(eSet)
    
}