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11
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1 require("BiocGenerics", quietly = TRUE)
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2 require("data.table", quietly = TRUE)
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3 require("GEOquery", quietly = TRUE)
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4 require("rtracklayer", quietly = TRUE)
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5
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6 options(warn = -1)
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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 IlmnTable = args[3]
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11 gmTable = args[4]
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12
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13 TAB = fread(GSMTable)
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14
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15 if (is.null(TAB)) {
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16 stop("Must specify input files")
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17 } else {
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18 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
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19 IlmnIDTable <- Table(GEODataTable)
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20 MetaData <- data.frame(Meta(GEODataTable))
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21
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22
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23 write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t")
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24 }
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25
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26 hm450.hg19 <- getPlatform()
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27
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28 IlmnInfo <-
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29 data.table(
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30 IlmnID = names(hm450.hg19),
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31 CHR = as.data.frame(hm450.hg19@seqnames)$value,
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32 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
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33 )
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34
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35
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36 write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t")
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37
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38
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39 if (length(TAB$ID) > 1) {
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40 mysamples <-
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41 do.call("data.table", lapply(TAB$ID[-1], function(x)
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42 Table(getGEO(x, getGPL = FALSE))[, -1]))
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43
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44 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
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45
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46 } else {
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47 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
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48 }
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49
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50
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51 write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")
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