Mercurial > repos > idot > coverage_correlation

comparison corr.R @ 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 7bdd29cdfed8
children ecad2cd5038f
comparison
equal deleted inserted replaced
5:9abd178b46bd 6:fcf85568a102
122 122
123 getCoverages <- function(infiles, formats){ 123 getCoverages <- function(infiles, formats){
124 apply(data.frame(file=infiles,format=formats),1, function(row){ getCoverage(row['file'], row['format']) }) 124 apply(data.frame(file=infiles,format=formats),1, function(row){ getCoverage(row['file'], row['format']) })
125 } 125 }
126 126
127 getMappable <- function(mappable){ 127 getMappable <- function(coverages, mappable){
128 if(is.na(mappable)){ 128 print(paste("creating mappability", mappable))
129 if(is.na(mappable)){
129 createMappable(coverages) 130 createMappable(coverages)
130 }else{ 131 }else{
131 import(mappable, format="bed", asRangedData = FALSE) 132 import(mappable, format="bed", asRangedData = FALSE)
132 } 133 }
133 } 134 }
148 print("parsed input parameters") 149 print("parsed input parameters")
149 print(lpp) 150 print(lpp)
150 151
151 152
152 coverages <- getCoverages(infiles, formats) 153 coverages <- getCoverages(infiles, formats)
153 mappability <- getMappable(mappable) 154 mappability <- getMappable(coverages, mappable)
154 155
155 calcAndPlot(coverages, outnames, mappability, outnamePDF, outnameMat,title) 156 calcAndPlot(coverages, outnames, mappability, outnamePDF, outnameMat,title)
156 157
157 158
158 159