--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findDMR/findDMR.R	Fri Apr 14 06:44:35 2017 -0400
@@ -0,0 +1,45 @@
+require("minfi", quietly = TRUE)
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+require("data.table", quietly = TRUE)
+
+
+args <- commandArgs(trailingOnly = TRUE)
+GSMTable = args[1]
+platform = args[2]
+Data_Table = args[3]
+cutoff = as.numeric(args[4])
+clusterSize = as.numeric(args[5])
+DMR = args[6]
+
+TAB = fread(GSMTable)
+
+IlmnInfo = fread(platform)
+
+gmSet = fread(Data_Table)
+
+# bumphunter Run with processed data
+designMatrix <- model.matrix( ~ TAB$Phenotype)
+
+bumps <- bumphunter(
+  as.matrix(gmSet),
+  design = designMatrix,
+  pos = IlmnInfo$BP,
+  cutoff = cutoff,
+  chr = IlmnInfo$CHR
+)
+
+# choose DMR's of a certain length threshold
+DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ]
+DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end)
+
+
+
+write.table(
+  DMRInfo,
+  DMR,
+  quote = F,
+  sep = "\t",
+  row.names = F,
+  col.names = F
+)