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Coverage Across Ranges

Source: R/coverage_ops.R
fast_coverage.Rd

Compute per-position coverage for input ranges.

Usage

fast_coverage(
  x,
  shift = 0L,
  width = NULL,
  weight = 1L,
  method = c("auto", "sort", "hash"),
  threads = fast_default_threads()
)

Arguments

x

An IRanges or GRanges object.

shift

Passed to coverage(). Use this to shift intervals before computing coverage.

width

Passed to coverage(). Use this to force the output length.

weight

Passed to coverage(). This can be a scalar or vector and is useful when intervals should contribute weighted counts instead of 1.

method

Coverage method.

threads

Integer scalar thread count. Reserved for API consistency.

Value

Rle (for IRanges) or RleList (for GRanges).

Details

Coverage answers the question: "how many ranges cover each position?"

For IRanges, the result is one Rle.

For GRanges, the result is an RleList, usually one coverage track per sequence level.

Examples

x <- IRanges::IRanges(start = c(1, 4, 10), end = c(5, 8, 12))
fast_coverage(x)
#> integer-Rle of length 12 with 5 runs
#>   Lengths: 3 2 3 1 3
#>   Values : 1 2 1 0 1