inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R

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

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

path <- system.file("testScripts/R", package="aroma.affymetrix")
pathname <- file.path(path, "downloadUtils.R")
source(pathname)

ar <- AromaRepository(verbose=TRUE)

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

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

pathname <- downloadCDF(ar, chipType)
verbose && cat(verbose, "CDF: ", pathname)

pathname <- downloadCDF(ar, chipType, tags=tags)
verbose && cat(verbose, "CDF: ", pathname)

# Affymetrix NetAffx CSV file
path <- "analysis/downloads/na35/genotyping"
pathnameS <- file.path(path, "GenomeWideSNP_6.na35.annot.csv")
pathname <- downloadAffymetrixNetAffxCsvFile(pathnameS)
verbose && cat(verbose, "NetAffx CSV: ", pathname)

pathnameS <- file.path(path, "GenomeWideSNP_6.cn.na35.annot.csv")
pathname <- downloadAffymetrixNetAffxCsvFile(pathnameS)
verbose && cat(verbose, "NetAffx CN CSV: ", pathname)

verbose && exit(verbose)