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6
|
1 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
|
|
9
|
2 require("data.table", quietly = TRUE)
|
|
0
|
3 require("minfi", quietly = TRUE)
|
|
|
4
|
|
6
|
5 options(warn = -1)
|
|
|
6 options("download.file.method"="wget")
|
|
0
|
7
|
|
|
8 args <- commandArgs(trailingOnly = TRUE)
|
|
|
9
|
|
6
|
10 input1 = args[1]
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|
|
11 input2 = args[2]
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|
|
12 output = args[3]
|
|
5
|
13
|
|
6
|
14 GRset <- get(load(input1))
|
|
0
|
15
|
|
6
|
16 pheno <- fread(input2)
|
|
|
17
|
|
|
18 designMatrix <- model.matrix(~ pheno$Phenotype)
|
|
0
|
19
|
|
6
|
20 dmrs <- bumphunter(GRset, design = designMatrix,
|
|
|
21 cutoff = 0.2, B=0, type="Beta")
|
|
|
22 write.table(dmrs, output)
|
