bed_closest | R Documentation |
Identify closest intervals.
bed_closest(x, y, overlap = TRUE, suffix = c(".x", ".y"))
x |
ivl_df |
y |
ivl_df |
overlap |
report overlapping intervals |
suffix |
colname suffixes in output |
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()
.
ivl_df with additional columns:
.overlap
amount of overlap with overlapping interval. Non-overlapping
or adjacent intervals have an overlap of 0. .overlap
will not be included
in the output if overlap = FALSE
.
.dist
distance to closest interval. Negative distances
denote upstream intervals. Book-ended intervals have a distance of 1.
For each interval in x bed_closest()
returns overlapping intervals from y
and the closest non-intersecting y interval. Setting overlap = FALSE
will
report the closest non-intersecting y intervals, ignoring any overlapping y
intervals.
https://bedtools.readthedocs.io/en/latest/content/tools/closest.html
Other multiple set operations:
bed_coverage()
,
bed_intersect()
,
bed_map()
,
bed_subtract()
,
bed_window()
x <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 100, 125
)
y <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 25, 50,
"chr1", 140, 175
)
bed_glyph(bed_closest(x, y))
x <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 500, 600,
"chr2", 5000, 6000
)
y <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 100, 200,
"chr1", 150, 200,
"chr1", 550, 580,
"chr2", 7000, 8500
)
bed_closest(x, y)
bed_closest(x, y, overlap = FALSE)
# Report distance based on strand
x <- tibble::tribble(
~chrom, ~start, ~end, ~name, ~score, ~strand,
"chr1", 10, 20, "a", 1, "-"
)
y <- tibble::tribble(
~chrom, ~start, ~end, ~name, ~score, ~strand,
"chr1", 8, 9, "b", 1, "+",
"chr1", 21, 22, "b", 1, "-"
)
res <- bed_closest(x, y)
# convert distance based on strand
res$.dist_strand <- ifelse(res$strand.x == "+", res$.dist, -(res$.dist))
res
# report absolute distances
res$.abs_dist <- abs(res$.dist)
res
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