bed_subtract: Subtract two sets of intervals.

In valr: Genome Interval Arithmetic

Subtract two sets of intervals.

Description

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)

bed_subtract(x, y, any = TRUE)

valr documentation built on Sept. 19, 2023, 1:07 a.m.