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10
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1 options("download.file.method.GEOquery"="wget")
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2 options(warn = -1)
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3
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4 args <- commandArgs(trailingOnly = TRUE)
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5 GSMTable = args[1]
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6 protocol = args[2]
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7 platform = args[3]
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8 Data_Table = args[4]
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9
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10 TAB = fread(GSMTable)
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11
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12 if (is.null(TAB)) {
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13 stop("Must specify input files")
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14 } else {
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15 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
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16 IlmnIDTable <- Table(GEODataTable)
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17 MetaData <- data.frame(Meta(GEODataTable))
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18
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19
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20 write.table(MetaData, protocol, row.names = FALSE, sep = "\t")
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21 }
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22
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23 hm450.hg19 <- getPlatform()
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24
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25 IlmnInfo <-
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26 data.table(
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27 IlmnID = names(hm450.hg19),
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28 CHR = as.data.frame(hm450.hg19@seqnames)$value,
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29 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
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30 )
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31
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32
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33 write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t")
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34
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35
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36 if (length(TAB$ID) > 1) {
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37 mysamples <-
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38 do.call("data.table", lapply(TAB$ID[-1], function(x)
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39 Table(getGEO(x, getGPL = FALSE))[, -1]))
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40
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41 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
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42
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43 } else {
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44 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
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45 }
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46
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47 write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t")
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48
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