bed_cluster {valr} | R Documentation |
The ouput .id
column can be used in downstream grouping operations. Default
max_dist = 0
means that both overlapping and book-ended intervals will be
clustered.
bed_cluster(x, max_dist = 0)
x |
|
max_dist |
maximum distance between clustered intervals. |
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 .id
column specifying sets of clustered intervals.
https://bedtools.readthedocs.io/en/latest/content/tools/cluster.html
Other single set operations:
bed_complement()
,
bed_flank()
,
bed_merge()
,
bed_partition()
,
bed_shift()
,
bed_slop()
x <- tibble::tribble(
~chrom, ~start, ~end,
'chr1', 100, 200,
'chr1', 180, 250,
'chr1', 250, 500,
'chr1', 501, 1000,
'chr2', 1, 100,
'chr2', 150, 200
)
bed_cluster(x)
# glyph illustrating clustering of overlapping and book-ended intervals
x <- tibble::tribble(
~chrom, ~start, ~end,
'chr1', 1, 10,
'chr1', 5, 20,
'chr1', 30, 40,
'chr1', 40, 50,
'chr1', 80, 90
)
bed_glyph(bed_cluster(x), label = '.id')