Mercurial > repos > testtool > find_dmr

comparison findDMR/findDMR.R @ 5:715d03e1fd83 draft

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author testtool
date Mon, 20 Mar 2017 06:51:59 -0400
parents 0d1957068766
children a0e3f4efb03f
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4:0d1957068766 5:715d03e1fd83
10 Data_Table = args[3] 10 Data_Table = args[3]
11 cutoff = as.numeric(args[4]) 11 cutoff = as.numeric(args[4])
12 clusterSize = as.numeric(args[5]) 12 clusterSize = as.numeric(args[5])
13 DMR = args[6] 13 DMR = args[6]
14 14
15 #GSMTable<-("test-data/input.csv")
16 TAB = fread(GSMTable) 15 TAB = fread(GSMTable)
17 #IlmnTable <- ("test-data/IlmnTable.csv") 16
18 IlmnInfo = fread(platform) 17 IlmnInfo = fread(platform)
19 #gmTable<-("test-data/gmTable.csv") 18
20 gmSet = fread(Data_Table) 19 gmSet = fread(Data_Table)
21 20
22 # bumphunter Run with processed data 21 # bumphunter Run with processed data
23 designMatrix <- model.matrix( ~ TAB$Phenotype) 22 designMatrix <- model.matrix( ~ TAB$Phenotype)
24 23
33 # choose DMR's of a certain length threshold 32 # choose DMR's of a certain length threshold
34 DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ] 33 DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ]
35 DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end) 34 DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end)
36 35
37 36
38 #DMR<-("test-data/DMR.bed") 37
39 write.table( 38 write.table(
40 DMRInfo, 39 DMRInfo,
41 DMR, 40 DMR,
42 quote = F, 41 quote = F,
43 sep = "\t", 42 sep = "\t",