bed_intersect: Identify intersecting intervals.

View source: R/bed_intersect.r

bed_intersectR Documentation

Identify intersecting intervals.

Description

Report intersecting intervals from x and y tbls. Book-ended intervals have .overlap values of 0 in the output.

Usage

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

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

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 Sept. 19, 2023, 1:07 a.m.