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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
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| 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) | |
| } |
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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)