Identify intervals within a specified distance.

Usage

bed_window(x, y, genome, ...)

Arguments

x: ivl_df
y: ivl_df, or a path or URL to a bigWig (.bw) or bigBed (.bb) file. When a file is supplied, only the windowed regions around x are read from it (local files and http(s):// URLs are both supported), avoiding the cost of loading the entire file.
genome: genome_df
...: params for bed_slop and bed_intersect

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().

Examples

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

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 60,     75
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 125
)

bed_glyph(bed_window(x, y, genome, both = 15))


x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 10, 100,
  "chr2", 200, 400,
  "chr2", 300, 500,
  "chr2", 800, 900
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 150,    400,
  "chr2", 230,    430,
  "chr2", 350,    430
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 500,
  "chr2", 1000
)

bed_window(x, y, genome, both = 100)
#> # A tibble: 4 × 7
#>   chrom start.x end.x start.y end.y .source .overlap
#>   <chr>   <dbl> <dbl>   <dbl> <dbl> <chr>      <int>
#> 1 chr2      200   400     230   430 1            200
#> 2 chr2      200   400     350   430 1             80
#> 3 chr2      300   500     230   430 1            200
#> 4 chr2      300   500     350   430 1             80

# `y` can be a bigWig/bigBed file path or `http(s)://` URL; only the
# windowed regions around `x` are read from the file
xf <- tibble::tribble(
  ~chrom, ~start,   ~end,
  "chr1", 4840000, 4841000
)

gf <- read_genome(valr_example("hg19.chrom.sizes.gz"))

bed_window(xf, valr_example("test.bb"), gf, both = 10000)
#> # A tibble: 1 × 16
#>   chrom start.x   end.x start.y   end.y name.y   score.y strand.y thickStart.y
#>   <chr>   <dbl>   <dbl>   <dbl>   <dbl> <chr>      <int> <chr>           <int>
#> 1 chr1  4840000 4841000 4797973 4836816 testgene       1 +             4797973
#> # ℹ 7 more variables: thickEnd.y <int>, reserved.y <int>, blockCount.y <int>,
#> #   blockSizes.y <chr>, chromStarts.y <chr>, .source <chr>, .overlap <int>

# add a `.dist` column to the output
if (FALSE) { # \dontrun{
bed_window(x, y, genome, both = 200) |>
 mutate(
   .dist = case_when(
     .overlap == 0 ~ abs(pmax(start.x, start.y) - pmin(end.x, end.y)),
     .default = 0
   )
 )
} # }

Identify intervals within a specified distance.

Usage

Arguments

Details

See also

Examples