# HG changeset patch
# User kpbioteam
# Date 1554391223 14400
# Node ID 2ee6ac5227f106c2a7255a094a16e20f63d8ab3b
# Parent  81a9b843e05c4c1eb5fdeea5e3312f9610c72255
Uploaded

diff -r 81a9b843e05c -r 2ee6ac5227f1 minfi_dmr.xml
--- a/minfi_dmr.xml	Thu Apr 04 11:20:00 2019 -0400
+++ b/minfi_dmr.xml	Thu Apr 04 11:20:23 2019 -0400
@@ -48,17 +48,10 @@
         nullMethod = nullMethod,
         B = B)
 
-dmrGR <- with(dmrs\$table,GRanges(chr,IRanges(start,end),area=area,value=value))
-
-dmrGR <- as.data.frame(dmrGR)
-
-colnames(dmrGR) <- c("seqnames","start","end","width","strand","area","value")
+dmrGR <- dmrs\$table[,c(1,2,3)] 
+colnames(dmrGR) <- c("chr","start","end")
 
-dmrGR\$strand <- NULL
-
-dmrGR\$area <- NULL
-
-write.table(dmrGR, file= '$dmr', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t")
+write.table(dmrGR, file= '$dmr', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t")
  ]]>
     </configfile>
     </configfiles>
@@ -99,12 +92,9 @@
 
 The output is an interval file with the following columns:
 
-    - seqnames
+    - chr
     - start
     - end
-    - width 
-    - area
-    - value
 
     ]]></help>
     <expand macro="citations" />