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