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12
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1 require("minfi", quietly = TRUE)
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2
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3 options(warn = -1)
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4 options("download.file.method"="wget")
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11
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5
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10
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6 args <- commandArgs(trailingOnly = TRUE)
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12
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7 input1 = args[1]
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8 input2 = args[2]
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9 cutoff = as.numeric(args[3])
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10 B = as.numeric(args[4])
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11 pickCutoffQ = as.numeric(args[5])
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12 output1 = args[6]
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13 output2 = args[7]
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0
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14
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12
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15 GRset <- get(load(input1))
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0
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16
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12
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17 pheno <- fread(input2)
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10
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18
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12
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19 designMatrix <- model.matrix(~ pheno$Phenotype)
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0
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20
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12
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21 dmrs <- bumphunter(GRset, design = designMatrix,
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22 cutoff =cutoff, B=B, type="Beta", pickCutoff=TRUE,
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23 pickCutoffQ=pickCutoffQ)
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24
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25 DMRTable <- dmrs$table
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26
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27 write.table(DMRTable, output1)
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0
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28
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12
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29 sign=sign(DMRTable$value)
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10
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30
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12
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31 sign[sign==-1]="-"
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32 sign[sign==1]="+"
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33
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34 dmr_track<-cbind(as.character(DMRTable$chr),DMRTable$start,DMRTable$end,sign)
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35
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36 write.table(dmr_track,output2,quote = FALSE, sep = "\t\t\t\t",row.names = FALSE, col.names = FALSE,append=TRUE) |
