Create flanking intervals from input intervals.

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_genomecov(), 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)
#> # A tibble: 2 × 6
#>   chrom start   end name  score strand
#>   <chr> <int> <int> <chr> <chr> <chr> 
#> 1 chr1    400   500 .     .     +     
#> 2 chr1    900  1000 .     .     -     

bed_flank(x, genome, right = 100)
#> # A tibble: 2 × 6
#>   chrom start   end name  score strand
#>   <chr> <int> <int> <chr> <chr> <chr> 
#> 1 chr1   1000  1100 .     .     +     
#> 2 chr1   1500  1600 .     .     -     

bed_flank(x, genome, both = 100)
#> # A tibble: 4 × 6
#>   chrom start   end name  score strand
#>   <chr> <int> <int> <chr> <chr> <chr> 
#> 1 chr1    400   500 .     .     +     
#> 2 chr1    900  1000 .     .     -     
#> 3 chr1   1000  1100 .     .     +     
#> 4 chr1   1500  1600 .     .     -     

bed_flank(x, genome, both = 0.5, fraction = TRUE)
#> # A tibble: 4 × 6
#>   chrom start   end name  score strand
#>   <chr> <int> <int> <chr> <chr> <chr> 
#> 1 chr1    250   500 .     .     +     
#> 2 chr1    750  1000 .     .     -     
#> 3 chr1   1000  1250 .     .     +     
#> 4 chr1   1500  1750 .     .     -