Skip to contents

Compute coverage of intervals.

Source: R/bed_coverage.R
bed_coverage.Rd

Compute coverage of intervals.

Usage

bed_coverage(x, y, ..., min_overlap = NULL)

Arguments

x

ivl_df

y

ivl_df

...

extra arguments (not used)

min_overlap

minimum overlap in base pairs required for the operation. Set to 1 to exclude book-ended intervals (matching bedtools behavior), or 0 to include them (legacy valr behavior). The default will change from 0 to 1 in a future version.

Value

ivl_df with the following additional columns:

  • .ints number of x intersections

  • .cov per-base coverage of x intervals

  • .len total length of y intervals covered by x intervals

  • .frac .len scaled by the number of y intervals

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

See also

https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html

Other multiple set operations: bed_closest(), bed_intersect(), bed_map(), bed_subtract(), bed_window()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~strand,
  "chr1", 100,    500,  "+",
  "chr2", 200,    400,  "+",
  "chr2", 300,    500,  "-",
  "chr2", 800,    900,  "-"
)

y <- tibble::tribble(
  ~chrom, ~start, ~end, ~value, ~strand,
  "chr1", 150,    400,  100,    "+",
  "chr1", 500,    550,  100,    "+",
  "chr2", 230,    430,  200,    "-",
  "chr2", 350,    430,  300,    "-"
)

bed_coverage(x, y)
#> Warning: The `min_overlap` argument of `bed_coverage()` is deprecated as of valr 0.8.0.
#> ℹ The default will change from 0 (book-ended intervals overlap) to 1 (strict
#>   overlap) in a future version.
#> ℹ Set `min_overlap = 0L` to keep the legacy behavior, or `min_overlap = 1L` for
#>   bedtools-compatible behavior.
#> # A tibble: 4 × 8
#>   chrom start   end strand .ints  .cov  .len .frac
#>   <chr> <dbl> <dbl> <chr>  <int> <int> <dbl> <dbl>
#> 1 chr1    100   500 +          2   250   400 0.625
#> 2 chr2    200   400 +          2   170   200 0.85 
#> 3 chr2    300   500 -          2   130   200 0.65 
#> 4 chr2    800   900 -          0     0   100 0