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view getMETAdata/getMETAdata.R @ 72:cb14dbc2fd60 draft

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author testtool
date Tue, 15 Aug 2017 06:06:55 -0400
parents 81b5c08c21e1
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require("GEOquery", quietly = TRUE)


options(warn = -1)
options("download.file.method"="wget")
args <- commandArgs(trailingOnly = TRUE)
GSMTable = args[1]
MetaTable = args[2]

TAB = read.table(GSMTable)


if (is.null(TAB)) {
  stop("Must specify input files")
} else {
  options(download.file.method.GEOquery = "wget") 


  GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
  MetaData <- data.frame(Meta(GEODataTable))

  write.table(MetaData, MetaTable, row.names = FALSE, sep = "\t")
}