bed_intersect: Identify intersecting intervals.

In valr: Genome Interval Arithmetic

Identify intersecting intervals.

Description

Report intersecting intervals from x and y tbls.

Usage

bed_intersect(
  x,
  ...,
  invert = FALSE,
  suffix = c(".x", ".y"),
  min_overlap = NULL
)

Arguments

x	ivl_df
...	one or more (e.g. a list of) y ivl_df()s
invert	report x intervals not in y
suffix	colname suffixes in output
min_overlap	minimum overlap in base pairs required for intersection. 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.

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().

Value

ivl_df with original columns from x and y suffixed with .x and .y, and a new .overlap column with the extent of overlap for the intersecting intervals.

If multiple y tbls are supplied, the .source contains variable names associated with each interval. All original columns from the y are suffixed with .y in the output.

If ... contains named inputs (i.e ⁠a = y, b = z⁠ or list(a = y, b = z)), then .source will contain supplied names (see examples).

See Also

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

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

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 25, 50,
  "chr1", 100, 125
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 30,     75
)

bed_glyph(bed_intersect(x, y))

bed_glyph(bed_intersect(x, y, invert = TRUE))

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

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

bed_intersect(x, y)

bed_intersect(x, y, invert = TRUE)

# start and end of each overlapping interval
res <- bed_intersect(x, y)
dplyr::mutate(res,
  start = pmax(start.x, start.y),
  end = pmin(end.x, end.y)
)

z <- tibble::tribble(
  ~chrom, ~start, ~end, ~value,
  "chr1", 150,    400,  100,
  "chr1", 500,    550,  100,
  "chr2", 230,    430,  200,
  "chr2", 750,    900,  400
)

bed_intersect(x, y, z)

bed_intersect(x, exons = y, introns = z)

# a list of tbl_intervals can also be passed
bed_intersect(x, list(exons = y, introns = z))

valr documentation built on Dec. 10, 2025, 9:08 a.m.