bed_flank: Create flanking intervals from input intervals.

View source: R/bed_flank.r

bed_flankR Documentation

Create flanking intervals from input intervals.

Description

Create flanking intervals from input intervals.

Usage

bed_flank(
  x,
  genome,
  both = 0,
  left = 0,
  right = 0,
  fraction = FALSE,
  strand = FALSE,
  trim = FALSE,
  ...
)

Arguments

x

ivl_df

genome

genome_df

both

number of bases on both sizes

left

number of bases on left side

right

number of bases on right side

fraction

define flanks based on fraction of interval length

strand

define left and right based on strand

trim

adjust coordinates for out-of-bounds intervals

...

extra arguments (not used)

Value

ivl_df

See Also

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

Other single set operations: bed_cluster(), bed_complement(), bed_merge(), bed_partition(), bed_shift(), bed_slop()

Examples

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

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 130
)

bed_glyph(bed_flank(x, genome, both = 20))

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~name, ~score, ~strand,
  "chr1", 500,    1000, ".",   ".",    "+",
  "chr1", 1000,   1500, ".",   ".",    "-"
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 5000
)

bed_flank(x, genome, left = 100)

bed_flank(x, genome, right = 100)

bed_flank(x, genome, both = 100)

bed_flank(x, genome, both = 0.5, fraction = TRUE)


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