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changeset 6:fcf85568a102

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dont know how this worked. added coverages to mappable
author Ido Tamir <ido.tamir@imp.ac.at>
date Sun, 18 Aug 2013 17:18:16 +0200
parents 9abd178b46bd
children cde608491511
files corr.R
diffstat 1 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/corr.R	Sun Aug 18 17:14:10 2013 +0200
+++ b/corr.R	Sun Aug 18 17:18:16 2013 +0200
@@ -124,8 +124,9 @@
    apply(data.frame(file=infiles,format=formats),1, function(row){ getCoverage(row['file'], row['format']) })
 }
 
-getMappable <- function(mappable){
-    if(is.na(mappable)){
+getMappable <- function(coverages, mappable){
+    print(paste("creating mappability", mappable))
+	if(is.na(mappable)){
 	    createMappable(coverages)
     }else{
         import(mappable, format="bed", asRangedData = FALSE)
@@ -150,7 +151,7 @@
 
 
 coverages <- getCoverages(infiles, formats)
-mappability <- getMappable(mappable)
+mappability <- getMappable(coverages, mappable)
 
 calcAndPlot(coverages, outnames, mappability, outnamePDF, outnameMat,title)