inst/tests/downloadData.R

In ShixiangWang/iProfile: integrated cancer Profile using multiple datasets

# Download raw data
setwd("~/projects/iProfile/")
require(GEOquery)

# several data has been downloaded
# so download others
GEO_IDs <- c("GSE68465", "GSE27716",
             "GSE17475", "GSE43580",
             "GSE50081", "GSE37745", "GSE28571")
# tars <- paste(GEO_IDs, "_RAW.tar", sep="")
for (i in 1:length(GEO_IDs)){
    # GEO_tar <- paste(GEO_IDs[i], tars[i], sep="/")
    getGEOSuppFiles(GEO=GEO_IDs[i], baseDir = "./inst/tests/iGCC/cel_files", makeDirectory = F)
}

# Download matrix data
# Use sample IDs as above
for (i in 1:length(GEO_IDs)){
    getGEO(GEO_IDs[i], destdir = "./inst/tests/iGCC/matrixSeries",
           GSEMatrix = TRUE, AnnotGPL = TRUE)
}