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Calculate coverage across a genome

Source: R/bed_genomecov.R
bed_genomecov.Rd

This function is useful for calculating interval coverage across an entire genome.

Usage

bed_genomecov(x, genome, zero_depth = FALSE)

Arguments

x

ivl_df

genome

genome_df

zero_depth

If TRUE, report intervals with zero depth. Zero depth intervals will be reported with respect to groups.

Value

ivl_df with the an additional column:

  • .depth depth of interval coverage

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/genomecov.html

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

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~strand,
  "chr1", 20, 70, "+",
  "chr1", 50, 100, "-",
  "chr1", 200, 250, "+",
  "chr1", 220, 250, "+"
)

genome <- tibble::tribble(
  ~chrom, ~size,
  "chr1", 500,
  "chr2", 1000
)

bed_genomecov(x, genome)
#> # A tibble: 5 × 4
#>   chrom start   end .depth
#>   <chr> <int> <int>  <int>
#> 1 chr1     20    50      1
#> 2 chr1     50    70      2
#> 3 chr1     70   100      1
#> 4 chr1    200   220      1
#> 5 chr1    220   250      2

bed_genomecov(dplyr::group_by(x, strand), genome)
#> # A tibble: 4 × 5
#>   chrom start   end strand .depth
#>   <chr> <int> <int> <chr>   <int>
#> 1 chr1     20    70 +           1
#> 2 chr1    200   220 +           1
#> 3 chr1    220   250 +           2
#> 4 chr1     50   100 -           1

bed_genomecov(dplyr::group_by(x, strand), genome, zero_depth = TRUE)
#> # A tibble: 11 × 5
#>    chrom start   end strand .depth
#>    <chr> <int> <dbl> <chr>   <int>
#>  1 chr1      0    20 +           0
#>  2 chr1      0    50 -           0
#>  3 chr1     20    70 +           1
#>  4 chr1     50   100 -           1
#>  5 chr1     70   200 +           0
#>  6 chr1    100   500 -           0
#>  7 chr1    200   220 +           1
#>  8 chr1    220   250 +           2
#>  9 chr1    250   500 +           0
#> 10 chr2      0  1000 +           0
#> 11 chr2      0  1000 -           0