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71
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1 require("data.table", quietly = TRUE)
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2 require("GEOquery", quietly = TRUE)
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3
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4
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5 options(warn = -1)
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6 options("download.file.method"="wget")
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7 args <- commandArgs(trailingOnly = TRUE)
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8 GSMTable = args[1]
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9 MetaTable = args[2]
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10
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11 TAB = fread(GSMTable)
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12
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13
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14 if (is.null(TAB)) {
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15 stop("Must specify input files")
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16 } else {
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17 options(download.file.method.GEOquery = "wget")
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18
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19
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20 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
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21 MetaData <- data.frame(Meta(GEODataTable))
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22
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23 write.table(MetaData, MetaTable, row.names = FALSE, sep = "\t")
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24 }
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25
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