Subtract two sets of intervals.

Subtract y intervals from x intervals.

Usage

bed_subtract(x, y, any = FALSE)

Arguments

x

ivl_df

y

ivl_df

any

remove any x intervals that overlap y

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/subtract.html

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

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1,      100
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 50,     75
)

bed_glyph(bed_subtract(x, y))


x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 100,    200,
  "chr1", 250,    400,
  "chr1", 500,    600,
  "chr1", 1000,   1200,
  "chr1", 1300,   1500
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 150,    175,
  "chr1", 510,    525,
  "chr1", 550,    575,
  "chr1", 900,    1050,
  "chr1", 1150,   1250,
  "chr1", 1299,   1501
)

bed_subtract(x, y)
#> # A tibble: 7 × 3
#>   chrom start   end
#>   <chr> <dbl> <dbl>
#> 1 chr1    100   150
#> 2 chr1    175   200
#> 3 chr1    250   400
#> 4 chr1    500   510
#> 5 chr1    525   550
#> 6 chr1    575   600
#> 7 chr1   1050  1150

bed_subtract(x, y, any = TRUE)
#> # A tibble: 1 × 3
#>   chrom start   end
#>   <chr> <dbl> <dbl>
#> 1 chr1    250   400