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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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4
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12
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5 options(warn = -1)
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17
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6 options("download.file.method"="wget")
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7
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12
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8 args <- commandArgs(trailingOnly = TRUE)
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9 DMR = args[1]
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10 annoPeakTable = args[2]
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11
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15
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12 #DMR <- ("test-data/DMR.bed")
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12
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13 DMRInfo = read.table(
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14 DMR,
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15 header = FALSE,
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16 sep = "\t",
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17 stringsAsFactors = FALSE,
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18 quote = ""
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19 )
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20
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14
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21 peaks <- GRanges(seqnames = DMRInfo[, 1],
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12
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22 ranges = IRanges
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23 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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17
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24
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14
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25 annoData <- toGRanges(EnsDb.Hsapiens.v75)
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26 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
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17
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27
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28 anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
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29
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15
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30 #annoPeakTable <- ('test-data/ChIPPeak.csv')
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17
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31 write.csv(anno, annoPeakTable, row.names = FALSE) |
