Mercurial > repos > idot > coverage_correlation

comparison corr.R @ 12:f3e037496c18

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its even checking the levels
author Ido Tamir <ido.tamir@imp.ac.at>
date Sun, 18 Aug 2013 21:33:43 +0200
parents 74bfa2464411
children de452b96da8e
comparison
equal deleted inserted replaced
11:74bfa2464411 12:f3e037496c18
144 144
145 changeSeqInfo <- function(coverages){ 145 changeSeqInfo <- function(coverages){
146 seqinfo <- mergeSeqInfo(coverages) 146 seqinfo <- mergeSeqInfo(coverages)
147 lapply(coverages, function(cov){ 147 lapply(coverages, function(cov){
148 si <- as.data.frame(cov@seqinfo) 148 si <- as.data.frame(cov@seqinfo)
149 si <- data.frame(chr=rownames(si), si) 149 si <- data.frame(chr=rownames(si), si, stringsAsFactors=FALSE)
150 sis <- subset(seqinfo, seqnames %in% si$chr) 150 sis <- subset(seqinfo, seqnames %in% si$chr)
151 sis <- sis[match(si$chr, sis$seqnames),]
151 si <- Seqinfo(seqnames=as.character(sis$seqnames), seqlengths=sis$seqlengths, isCircular=sis$isCircular, genome=sis$genome) 152 si <- Seqinfo(seqnames=as.character(sis$seqnames), seqlengths=sis$seqlengths, isCircular=sis$isCircular, genome=sis$genome)
152 cov@seqinfo <- si 153 cov@seqinfo <- si
153 cov 154 cov
154 }) 155 })
155 } 156 }
156 157
157 args <- commandArgs(TRUE) 158 args <- commandArgs(TRUE)