GetPercentOverlap.R

library(GenomicRanges)
library(matrixStats)

ranges1 <- GRanges(seqnames = c("chr1", "chr2", "chr3"),
                   ranges = IRanges(start=c(1,100,1000),
                                    end = c(10,150,5000)))

ranges2 <- GRanges(seqnames = c("chr1", "chr2", "chr3"),
                   ranges = IRanges(start=c(11,110,2000),
                                    end = c(20,130,3000)))

GetPercentOverlap <- function(query,
                              subject){
  
  #/ find overlap positions
  ovlap <- findOverlaps(query, subject)
  
  #/ subset the input ranges to those ranges that have overlaps with the second ranges object
  r1 <- ranges(query[ovlap@from] )
  r2 <- ranges(subject[ovlap@to])
  
  #/ new GRanges object only with the overlapping intervals
  gr<-
  GRanges(seqnames = as.character(seqnames(query[ovlap@from])),
          ranges = IRanges(start = matrixStats::rowMaxs(as.matrix(data.frame(r1=start(r1), r2=start(r2)))),
                           end = matrixStats::rowMins(as.matrix(data.frame(r1=end(r1), r2=end(r2))))))
  
  mcols(gr)$percentOverlap <- 100 * width(gr) / width(r1)
  
  #/ add original query ranges
  ranges(gr) <- ranges(r1)
  
  #/ add subject coordinates to mcols(gr)
  mcols(gr)$subject <- r2
  gr
}