inst/testScripts/futures/GenomeWideSNP_6/01a.downloadAnnotationData.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

library("aroma.core")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
ar <- AromaRepository(verbose=TRUE)

verbose && enter(verbose, "Downloading annotation data")

chipType <- "GenomeWideSNP_6"
tags <- "Full"
verbose && cat(verbose, "Chip type: ", chipType)

pathname <- downloadACS(ar, chipType, tags=".*")
verbose && cat(verbose, "ACS: ", pathname)

for (tags in list(NULL, "Full")) {
  pathname <- downloadCDF(ar, chipType, tags=tags)
  verbose && cat(verbose, "CDF: ", pathname)

  pathname <- downloadUFL(ar, chipType, tags=c(tags, ".*"))
  verbose && cat(verbose, "UFL: ", pathname)

  pathname <- downloadUGP(ar, chipType, tags=c(tags, ".*"))
  verbose && cat(verbose, "UGP: ", pathname)

  pathname <- downloadUGC(ar, chipType, tags=c(tags, ".*"))
  verbose && cat(verbose, "UGC: ", pathname)
}

verbose && exit(verbose)