# HG changeset patch
# User kpbioteam
# Date 1554391279 14400
# Node ID 3d083550977fbab41ed66f7c6bef6a372b875237
# Parent 2ee6ac5227f106c2a7255a094a16e20f63d8ab3b
Uploaded
diff -r 2ee6ac5227f1 -r 3d083550977f minfi_dmp.xml
--- a/minfi_dmp.xml Thu Apr 04 11:20:23 2019 -0400
+++ b/minfi_dmp.xml Thu Apr 04 11:21:19 2019 -0400
@@ -29,13 +29,9 @@
tab <- tab[,-(11:14),drop=FALSE]
-colnames(tab) <- c("seqname","source","feature","start","end","score","strand", "frame","attributes", "names")
-
-tab[,"source"] <- NULL
+tab <- tab[,c(1,4,5,10)]
-tab[,"frame"] <- NULL
-
-tab[,"attributes"] <- NULL
+colnames(tab) <- c('chr','start','end','names')
dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar)
@@ -43,10 +39,10 @@
data <- merge(dmp, tab, by="names",sort = TRUE)
-data <- data[c("seqname","start","end","names","score","strand", "feature","intercept", "f", "pval","qval")]
+data <- data[,c(6,7,8,1,4,5)]
-write.table(data, file= '$dmp', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t")
- ]]>
+write.table(data, file= '$dmp', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t")
+]]>
@@ -56,13 +52,13 @@
-
+
-
+
@@ -80,17 +76,12 @@
The output is an interval file with the following columns:
- - seqnames
+ - chr
- start
- end
- - cpg
- names
- - score
- - strand
- - feature
- - intercept
- - f pval
- - qval
+ - pvalue
+ - qval
]]>