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comparison findDMR/findDMR.R @ 33:2c799524e1d3 draft

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author testtool
date Fri, 14 Apr 2017 06:44:35 -0400
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32:be1ca0e7829b 33:2c799524e1d3
1 require("minfi", quietly = TRUE)
2 require("ChIPseeker", quietly = TRUE)
3 require("ChIPpeakAnno", quietly = TRUE)
4 require("data.table", quietly = TRUE)
5
6
7 args <- commandArgs(trailingOnly = TRUE)
8 GSMTable = args[1]
9 platform = args[2]
10 Data_Table = args[3]
11 cutoff = as.numeric(args[4])
12 clusterSize = as.numeric(args[5])
13 DMR = args[6]
14
15 TAB = fread(GSMTable)
16
17 IlmnInfo = fread(platform)
18
19 gmSet = fread(Data_Table)
20
21 # bumphunter Run with processed data
22 designMatrix <- model.matrix( ~ TAB$Phenotype)
23
24 bumps <- bumphunter(
25 as.matrix(gmSet),
26 design = designMatrix,
27 pos = IlmnInfo$BP,
28 cutoff = cutoff,
29 chr = IlmnInfo$CHR
30 )
31
32 # choose DMR's of a certain length threshold
33 DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ]
34 DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end)
35
36
37
38 write.table(
39 DMRInfo,
40 DMR,
41 quote = F,
42 sep = "\t",
43 row.names = F,
44 col.names = F
45 )