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CDFpackages_installation

installCDFpkgs_run.R

This is the script used to install CDF packages from BrainArray (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp)

  • args[1] is the path to the folder, namely mapping_genes, containing BrainArrayMapping_withGPL_version.csv
  • args[2] is string indicating version of ENTREZG e.g. "25" (the latest version)
  • args[3] is a comma separted list of organism name(s)we want the packages for e.g. "Mus musculus,Homo sapiens"

Example: downloading and installing CDF packages version 25 for human and mouse data

Rscript installCDFpkgs_run.R path/to/mapping_genes "25" "Mus musculus,Homo sapiens"

Note: all the arguments must be specified for the script to run