get O/E ration and CpG ratio and GC content for given GRanges object and BSgenome. Returns a matrix of O/E ratio, CpGcontent and GC content

getOE.R

require(GenomicRanges)
require(Biostrings)


#' get OE ratio and GC content for a given set of DNAstrings
getOE.strset<-function(str.set)
{
  di.mat=dinucleotideFrequency(  str.set )
  a.mat =alphabetFrequency( str.set ,baseOnly=TRUE )
  exp=(a.mat[,2]*a.mat[,3])/width(str.set )
  obs=di.mat[,"CG"]
  OE=obs/exp
  
  cbind(oe=OE,CpGcont=obs/(width(str.set)-1),gc=100*(a.mat[,2]+a.mat[,3])/rowSums(a.mat[,1:4])   )
  
}


#' get  OE ratio and GC content for a given set of targetgenes
#' @param wins GRanges object
#' @param bs BSgenome object
getOE.gr<-function(wins,bs)
{
  str.set=getSeq(bs,wins)
  getOE.strset(str.set)
}  

library(devtools)
source_url("https://gist.github.com/al2na/8558751/raw/186547f599175d6958ce547c806c4317f453483a/getOE.R")

#' wins: GRanges object
#' bs: BSgenome object

' example

getOE.gr(wins,bs=Mmusculus)