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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 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
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6
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7 options("download.file.method"="wget")
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8 options(warn = -1)
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9
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10 args <- commandArgs(trailingOnly = TRUE)
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11 GSMTable = args[1]
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12 MetaTable = args[2]
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13 IlmnTable = args[3]
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14 gmTable = args[4]
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15
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16 TAB = fread(GSMTable)
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17
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18 if (is.null(TAB)) {
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19 stop("Must specify input files")
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20 } else {
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21 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
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22 IlmnIDTable <- Table(GEODataTable)
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23 MetaData <- data.frame(Meta(GEODataTable))
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24
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25
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26 write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t")
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27 }
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28
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29 hm450.hg19 <- getPlatform()
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30
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31 IlmnInfo <-
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32 data.table(
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33 IlmnID = names(hm450.hg19),
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34 CHR = as.data.frame(hm450.hg19@seqnames)$value,
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35 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
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36 )
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37
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38
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39 write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t")
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40
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41
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42 if (length(TAB$ID) > 1) {
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43 mysamples <-
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44 do.call("data.table", lapply(TAB$ID[-1], function(x)
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45 Table(getGEO(x, getGPL = FALSE))[, -1]))
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46
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47 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
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48
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49 } else {
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50 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
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51 }
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52
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53
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54 write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")
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