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1 require("minfi", quietly = TRUE)
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2 require("ChIPseeker", quietly = TRUE)
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3 require("ChIPpeakAnno", quietly = TRUE)
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4 require("data.table", quietly = TRUE)
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5
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6
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7 args <- commandArgs(trailingOnly = TRUE)
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8 GSMTable = args[1]
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9 IlmnTable = args[2]
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10 gmTable = args[3]
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11 cutoff = as.numeric(args[4])
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12 clusterSize = as.numeric(args[5])
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13 DMR = args[6]
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14
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15 #GSMTable<-("test-data/input.csv")
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16 TAB = fread(GSMTable)
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17 #IlmnTable <- ("test-data/IlmnTable.csv")
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18 IlmnInfo = fread(IlmnTable)
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19 #gmTable<-("test-data/gmTable.csv")
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20 gmSet = fread(gmTable)
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21
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22 # bumphunter Run with processed data
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23 designMatrix <- model.matrix( ~ TAB$Phenotype)
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24
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25 bumps <- bumphunter(
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26 as.matrix(gmSet),
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27 design = designMatrix,
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28 pos = IlmnInfo$BP,
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29 cutoff = cutoff,
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30 chr = IlmnInfo$CHR
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31 )
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32
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33 # choose DMR's of a certain length threshold
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34 DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ]
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35 DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end)
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36
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37
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38 #DMR<-("test-data/DMR.bed")
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39 write.table(
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40 DMRInfo,
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41 DMR,
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42 quote = F,
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43 sep = "\t",
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44 row.names = F,
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45 col.names = F
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46 )
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