bed_flank {valr} | R 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 |
|
genome |
|
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 |
trim |
adjust coordinates for out-of-bounds intervals |
... |
extra arguments (not used) |
Value
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)
bed_flank(x, genome, right = 100)
bed_flank(x, genome, both = 100)
bed_flank(x, genome, both = 0.5, fraction = TRUE)
[Package valr version 0.8.1 Index]