Select intervals bounded by a genome.

Used to remove out-of-bounds intervals, or trim interval coordinates using a genome.

Usage

bound_intervals(x, genome, trim = FALSE)

Arguments

x

ivl_df

genome

genome_df

trim

adjust coordinates for out-of-bounds intervals

Value

ivl_df

See also

Other utilities: bed12_to_exons(), bed_makewindows(), flip_strands(), interval_spacing()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", -100,   500,
  "chr1", 100,    1e9,
  "chr1", 500,    1000
)

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

# out-of-bounds are removed by default ...
bound_intervals(x, genome)
#> # A tibble: 1 × 3
#>   chrom start   end
#>   <chr> <dbl> <dbl>
#> 1 chr1    500  1000

# ... or can be trimmed within the bounds of a genome
bound_intervals(x, genome, trim = TRUE)
#> # A tibble: 3 × 3
#>   chrom start       end
#>   <chr> <dbl>     <dbl>
#> 1 chr1      0       500
#> 2 chr1    100 249250621
#> 3 chr1    500      1000