Search code examples
rloopsncbi

Loading multiple GSM files into R with a loop?

I’m trying to load multiple GSM files into R via a loop, but I think that I’m missing something obvious.

#Use i to loop through NCBI files GSM9714940 through GSM971948

for (i in 971940:971948){
  (GSMName <- paste("GSM", i, sep = "")) #Define the actual file name as found on NCBI
  GSMName <- getGEO(GSMName, destdir=".") #Use GSMName variable to pull data from NCBI 
  #This doesn't work b/c I'm using a variable to redefine itself, but
  #I need the NCBI file name to also be the variable name
  }
Solution

  • You can use assign():

    for (i in 971940:971948){
  GSMName <- paste("GSM", i, sep = "") 
  assign(GSMName, getGEO(GSMName, destdir="."))
}