This operation is similar to bedtools cluster. It reports each set of
overlapping or “book-ended” features in an interval file.
cluster_bed(x, max_dist = 0)
| x | A |
|---|---|
| max_dist | Maximum distance between features allowed for features to be merged. Default is 0. That is, overlapping and/or book-ended features are merged. |
A GRanges. Compared
Manual page of bedtools cluster:
https://bedtools.readthedocs.io/en/latest/content/tools/cluster.html
tbl <- read_bed(system.file("extdata", "example_merge.bed", package = "bedtorch"), use_gr = FALSE) # Basic usage clustered <- cluster_bed(tbl) head(clustered) #> chrom start end score cluster #> 1: 21 3 6 8 1 #> 2: 21 10 16 5 2 #> 3: 21 12 17 4 2 #> 4: 21 15 22 5 2 #> 5: 21 22 25 7 2 #> 6: 21 26 30 7 3 #> ------- #> genome: unspecified. # Change the maximum distance allowed clustered <- cluster_bed(tbl, max_dist = 10) head(clustered) #> chrom start end score cluster #> 1: 21 3 6 8 1 #> 2: 21 10 16 5 1 #> 3: 21 12 17 4 1 #> 4: 21 15 22 5 1 #> 5: 21 22 25 7 1 #> 6: 21 26 30 7 1 #> ------- #> genome: unspecified.