valr (version 0.8.3)

bed_cluster: Cluster neighboring intervals.

Description

The output .id column can be used in downstream grouping operations. Default max_dist = 0 means that both overlapping and book-ended intervals will be clustered.

Usage

bed_cluster(x, max_dist = 0)

Value

ivl_df with .id column specifying sets of clustered intervals.

Arguments

x

ivl_df

max_dist

maximum distance between clustered intervals.

Details

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().

See Also

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

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

Examples

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")