Tile-Based Coverage Summary — fast_tile

Aggregate coverage into fixed-width tiles.

Usage

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

Arguments

x: An IRanges or GRanges object.
tile_width: Integer scalar tile width.
step_width: Integer scalar step width. Use a value smaller than tile_width for overlapping tiles and the same value for adjacent tiles.
shift: Passed to coverage().
width: Passed to coverage().
weight: Passed to coverage().
method: Coverage method.
threads: Integer scalar thread count. Reserved for API consistency.

Value

A data.frame with tile coordinates and coverage_sum.

Details

fast_tile_coverage() converts base-resolution coverage into a simpler table of fixed-width summaries.

Each row in the result is one tile.

coverage_sum is the sum of coverage values across that tile.

For GRanges, the output also includes seqnames.

Examples

x <- IRanges::IRanges(start = c(1, 4, 10), end = c(5, 8, 12))
fast_tile_coverage(x, tile_width = 5L)
#>   start end coverage_sum
#> 1     1   5            7
#> 2     6  10            4
#> 3    11  12            2