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

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

Arguments

x

tbl_interval()

...

one or more (e.g. a list of) y tbl_interval()s

invert

report x intervals not in y

suffix

colname suffixes in output

Value

tbl_interval() 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).

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

Examples

x <- trbl_interval( ~chrom, ~start, ~end, 'chr1', 25, 50, 'chr1', 100, 125 ) y <- trbl_interval( ~chrom, ~start, ~end, 'chr1', 30, 75 ) bed_glyph(bed_intersect(x, y))
bed_glyph(bed_intersect(x, y, invert = TRUE))
x <- trbl_interval( ~chrom, ~start, ~end, 'chr1', 100, 500, 'chr2', 200, 400, 'chr2', 300, 500, 'chr2', 800, 900 ) y <- trbl_interval( ~chrom, ~start, ~end, ~value, 'chr1', 150, 400, 100, 'chr1', 500, 550, 100, 'chr2', 230, 430, 200, 'chr2', 350, 430, 300 ) bed_intersect(x, y)
#> # A tibble: 6 x 7 #> chrom start.x end.x start.y end.y value.y .overlap #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> #> 1 chr1 100 500 150 400 100 250 #> 2 chr1 100 500 500 550 100 0 #> 3 chr2 200 400 230 430 200 170 #> 4 chr2 200 400 350 430 300 50 #> 5 chr2 300 500 230 430 200 130 #> 6 chr2 300 500 350 430 300 80
bed_intersect(x, y, invert = TRUE)
#> # A tibble: 1 x 3 #> chrom start end #> <chr> <dbl> <dbl> #> 1 chr2 800 900
# 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))
#> # A tibble: 6 x 9 #> chrom start.x end.x start.y end.y value.y .overlap start end #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <dbl> <dbl> #> 1 chr1 100 500 150 400 100 250 150 400 #> 2 chr1 100 500 500 550 100 0 500 500 #> 3 chr2 200 400 230 430 200 170 230 400 #> 4 chr2 200 400 350 430 300 50 350 400 #> 5 chr2 300 500 230 430 200 130 300 430 #> 6 chr2 300 500 350 430 300 80 350 430
z <- trbl_interval( ~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)
#> # A tibble: 11 x 8 #> chrom start.x end.x start.y end.y value.y .source .overlap #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <int> #> 1 chr1 100 500 150 400 100 y 250 #> 2 chr1 100 500 150 400 100 z 250 #> 3 chr1 100 500 500 550 100 y 0 #> 4 chr1 100 500 500 550 100 z 0 #> 5 chr2 200 400 230 430 200 y 170 #> 6 chr2 200 400 230 430 200 z 170 #> 7 chr2 200 400 350 430 300 y 50 #> 8 chr2 300 500 230 430 200 y 130 #> 9 chr2 300 500 230 430 200 z 130 #> 10 chr2 300 500 350 430 300 y 80 #> 11 chr2 800 900 750 900 400 z 100
bed_intersect(x, exons = y, introns = z)
#> # A tibble: 11 x 8 #> chrom start.x end.x start.y end.y value.y .source .overlap #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <int> #> 1 chr1 100 500 150 400 100 exons 250 #> 2 chr1 100 500 150 400 100 introns 250 #> 3 chr1 100 500 500 550 100 exons 0 #> 4 chr1 100 500 500 550 100 introns 0 #> 5 chr2 200 400 230 430 200 exons 170 #> 6 chr2 200 400 230 430 200 introns 170 #> 7 chr2 200 400 350 430 300 exons 50 #> 8 chr2 300 500 230 430 200 exons 130 #> 9 chr2 300 500 230 430 200 introns 130 #> 10 chr2 300 500 350 430 300 exons 80 #> 11 chr2 800 900 750 900 400 introns 100
# a list of tbl_intervals can also be passed bed_intersect(x, list(exons = y, introns = z))
#> # A tibble: 11 x 8 #> chrom start.x end.x start.y end.y value.y .source .overlap #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <int> #> 1 chr1 100 500 150 400 100 exons 250 #> 2 chr1 100 500 150 400 100 introns 250 #> 3 chr1 100 500 500 550 100 exons 0 #> 4 chr1 100 500 500 550 100 introns 0 #> 5 chr2 200 400 230 430 200 exons 170 #> 6 chr2 200 400 230 430 200 introns 170 #> 7 chr2 200 400 350 430 300 exons 50 #> 8 chr2 300 500 230 430 200 exons 130 #> 9 chr2 300 500 230 430 200 introns 130 #> 10 chr2 300 500 350 430 300 exons 80 #> 11 chr2 800 900 750 900 400 introns 100