Mercurial > repos > testtool > find_dmr
comparison findDMR/findDMR.R @ 5:715d03e1fd83 draft
Uploaded
| 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", |