Dear all, 

I try to subtract one coverage from another and set the negative value in the result coverage object to 0 so that the coverage at each position would be a non-negative value.  I want all the negative values in <cov.gr2> object to be zero in this dummy example.

Thanks very much for your help!

Zhenhua Hu

library(GenomicRanges)
gr1 <- GRanges(seqnames = Rle(c("chr1", "chr2"), c(2,2)), ranges = IRanges(start = c(3,6,1,9), width = c(100, 200, 10, 40)))

cov.gr1 <- coverage(gr1)
cov.gr2 <-cov.gr1 * 0.5 - cov.gr1
cov.gr2

> cov.gr2
RleList of length 2
$chr1
numeric-Rle of length 205 with 4 runs
  Lengths:    2    3   97  103
  Values :    0 -0.5   -1 -0.5

$chr2
numeric-Rle of length 48 with 3 runs
  Lengths:    8    2   38
  Values : -0.5   -1 -0.5

Subset and replace as you might a regular vector

cov.gr2[cov.gr2 < 0] = 0