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1 require("ChIPseeker", quietly = TRUE)
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2 require("ChIPpeakAnno", quietly = TRUE)
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3
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4 options(warn = -1)
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5
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6 args <- commandArgs(trailingOnly = TRUE)
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7 DMR = args[1]
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8 annoPeakFigure = args[2]
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9
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10 #DMR <- ("test-data/DMR.bed")
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11 DMRInfo = read.table(
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12 DMR,
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13 header = FALSE,
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14 sep = "\t",
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15 stringsAsFactors = FALSE,
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16 quote = ""
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17 )
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18
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19 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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20 ranges = IRanges
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21 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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22
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23 annotatePeak <- (annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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24
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25 #annoPeakFigure <- ('test-data/annoPeakFigure.png')
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26
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27 png(file = annoPeakFigure,
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28 width = 1200,
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29 height = 600)
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30
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31 upsetplot(annotatePeak, vennpie = TRUE)
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32
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33 dev.off()
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