Mercurial > repos > testtool > find_dmr

comparison findDMR/findDMR.R @ 11:24ac6f93cc3e draft

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author testtool
date Thu, 11 May 2017 11:26:02 -0400
parents 7df2b7d79391
children 083895dbc289
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10:7df2b7d79391 11:24ac6f93cc3e
1 require("BiocGenerics", quietly = TRUE)
2 require("data.table", quietly = TRUE)
3 require("bumphunter", quietly = TRUE)
4
1 args <- commandArgs(trailingOnly = TRUE) 5 args <- commandArgs(trailingOnly = TRUE)
2 GSMTable = args[1] 6 GSMTable = args[1]
3 platform = args[2] 7 platform = args[2]
4 Data_Table = args[3] 8 Data_Table = args[3]
5 cutoff = as.numeric(args[4]) 9 cutoff = as.numeric(args[4])
26 # choose DMR's of a certain length threshold 30 # choose DMR's of a certain length threshold
27 DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ] 31 DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ]
28 DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end) 32 DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end)
29 33
30 34
31
32 write.table( 35 write.table(
33 DMRInfo, 36 DMRInfo,
34 DMR, 37 DMR,
35 quote = F, 38 quote = F,
36 sep = "\t", 39 sep = "\t",