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16
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1 require("ChIPseeker", quietly = TRUE)
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2 require("ChIPpeakAnno", quietly = TRUE)
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3 require("EnsDb.Hsapiens.v75", quietly = TRUE)
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19
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4 require("EnsDb.Mmusculus.v75", quietly = TRUE)
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16
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5
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12
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6 options(warn = -1)
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17
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7 options("download.file.method"="wget")
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8
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19
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9 args <- commandArgs(trailingOnly = TRUE)
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12
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10 DMR = args[1]
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19
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11 annoData = args[2]
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12 bindingType = args[3]
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13 upstream = as.numeric(args[4])
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14 downstream = as.numeric(args[5])
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15 ignore = args[6]
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16 annoPeakTable = args[7]
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12
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17
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19
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18 #DMR <- ("test-data/DMR.bed")
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19 DMRInfo = read.table(
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12
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20 DMR,
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21 header = FALSE,
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22 sep = "\t",
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23 stringsAsFactors = FALSE,
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24 quote = ""
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25 )
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26
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14
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27 peaks <- GRanges(seqnames = DMRInfo[, 1],
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12
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28 ranges = IRanges
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29 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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17
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30
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19
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31
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32 if (annoData == "human"){
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33 annoData <- toGRanges(EnsDb.Hsapiens.v75)
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34 } else {
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35 annoData <- toGRanges(EnsDb.Mmusculus.v75)
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36 }
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14
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37 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
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17
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38
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19
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39 if (ignore == "true"){
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40 x <- TRUE
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41 } else {
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42 x <- FALSE
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43 }
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44
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17
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45
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19
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46 if (bindingType =="startSite"){
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47 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("startSite"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
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48 } else if (bindingType =="endSite"){
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49 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("endSite"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
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50 } else {
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51 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("fullRange"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
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52 }
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53
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54
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55 write.table(anno, annoPeakTable, row.names = FALSE)
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