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1 require("ChIPseeker", quietly = TRUE)
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2 require("ChIPpeakAnno", quietly = TRUE)
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3 options(warn = -1)
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4
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5 args <- commandArgs(trailingOnly = TRUE)
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6 DMR = args[1]
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7 annoPeakTable = args[2]
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8
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9
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10 DMRInfo = read.table(
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11 DMR,
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12 header = FALSE,
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13 sep = "\t",
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14 stringsAsFactors = FALSE,
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15 quote = ""
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16 )
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17
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18 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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19 ranges = IRanges
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20 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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21
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22 annotatePeak <-
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23 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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24
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25
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26 write.csv(annotatePeak, annoPeakTable, row.names = FALSE)
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