Compute coverage over a Ranges object
compute_coverage(x, shift, width, weight, ...)a Ranges object
shift how much should each range in x be shifted by? (default = 0L)
width how long should the returned coverage score be? This must be either a positive integer or NULL (default = NULL)
weight how much weight should be assigned to each range? Either an integer or numeric vector or a column in x. (default = 1L)
other optional parameters to pass to coverage
An expanded Ranges object with a score column corresponding to the coverage value over that interval. Note that compute_coverage drops metadata associated with the orginal ranges.
IRanges::coverage(),
GenomicRanges::coverage()
rng <- as_iranges(data.frame(start = 1:10, width = 5))
compute_coverage(rng)
#> IRanges object with 9 ranges and 1 metadata column:
#> start end width | score
#> <integer> <integer> <integer> | <integer>
#> [1] 1 1 1 | 1
#> [2] 2 2 1 | 2
#> [3] 3 3 1 | 3
#> [4] 4 4 1 | 4
#> [5] 5 10 6 | 5
#> [6] 11 11 1 | 4
#> [7] 12 12 1 | 3
#> [8] 13 13 1 | 2
#> [9] 14 14 1 | 1
compute_coverage(rng, shift = 14L)
#> IRanges object with 10 ranges and 1 metadata column:
#> start end width | score
#> <integer> <integer> <integer> | <integer>
#> [1] 1 14 14 | 0
#> [2] 15 15 1 | 1
#> [3] 16 16 1 | 2
#> [4] 17 17 1 | 3
#> [5] 18 18 1 | 4
#> [6] 19 24 6 | 5
#> [7] 25 25 1 | 4
#> [8] 26 26 1 | 3
#> [9] 27 27 1 | 2
#> [10] 28 28 1 | 1
compute_coverage(rng, width = 10L)
#> IRanges object with 5 ranges and 1 metadata column:
#> start end width | score
#> <integer> <integer> <integer> | <integer>
#> [1] 1 1 1 | 1
#> [2] 2 2 1 | 2
#> [3] 3 3 1 | 3
#> [4] 4 4 1 | 4
#> [5] 5 10 6 | 5