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12
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1 require("ChIPseeker", quietly = TRUE)
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2 require("ChIPpeakAnno", quietly = TRUE)
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13
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3
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12
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4 options(warn = -1)
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13
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5 options("download.file.method"="wget")
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12
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6
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7 args <- commandArgs(trailingOnly = TRUE)
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8 DMR = args[1]
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9 annoPeakTable = args[2]
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10
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13
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11 DMR <- ("test-data/DMR.bed")
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12
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12 DMRInfo = read.table(
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13 DMR,
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14 header = FALSE,
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15 sep = "\t",
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16 stringsAsFactors = FALSE,
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17 quote = ""
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18 )
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19
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20 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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21 ranges = IRanges
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22 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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23
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13
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24 annotatePeak <-
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25 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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12
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26
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13
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27 annoPeakTable <- ('test-data/annoPeakTable.csv')
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12
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28 write.csv(annotatePeak, annoPeakTable, row.names = FALSE)
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