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Calculate Genomic Region Density

Source: R/genomic-helper.R
genomic_density.Rd

Computes the density or count of genomic regions in sliding or fixed windows across the genome. The density can be reported as the percentage of uncovered bases or the number of overlapping regions within each window.

Usage

genomic_density(
  region,
  window_size = 1e+07,
  n_window = NULL,
  overlap = TRUE,
  mode = c("coverage", "count"),
  seqlengths = NULL
)

Arguments

region

A data frame with at least 3 columns: chromosome, start, and end.

  • Column 1: character or factor, chromosome name.

  • Column 2: numeric, start position (must be <= end).

  • Column 3: numeric, end position.

window_size

Numeric, the width of each window (default is 1e+07). Ignored if n_window is specified.

n_window

Integer, the number of windows per chromosome. If provided, overrides window_size and evenly splits the chromosome into n_window (non-overlapping) or 2*n_window - 1 (overlapping) windows.

overlap

Logical, whether to use overlapping windows (default TRUE). Overlapping windows are spaced by half the window size.

mode

Character, either "coverage" or "count":

  • "count": reports the number of regions overlapping each window.

  • "coverage": reports the fraction of each window covered by regions.

seqlengths

Optional named vector of chromosome lengths. If missing, the maximum end value in the input is used as the chromosome length.

Value

A data frame with columns:

  • seqnames: The sequence (e.g., chromosome) names.

  • start: start of each window

  • end: end of each window

  • density: the region count or covered percent, depending on mode

Details

This function splits the input by chromosome and tiles the genomic space into windows, optionally overlapping. For each window, it calculates:

  • the number of regions that overlap it (if mode = "count"), or

  • the fraction of bases covered by any region (if mode = "percent").

Examples

region <- data.frame(
    chr = rep("chr1", 3),
    start = c(100, 5000000, 15000000),
    end = c(2000000, 7000000, 17000000)
)
genomic_density(region, window_size = 1e7, mode = "count")
#>   seqnames   start      end density
#> 1     chr1       1 10000000       2
#> 2     chr1 5000001 15000000       2
genomic_density(region, n_window = 3, overlap = FALSE, mode = "coverage")
#>   seqnames    start      end   density
#> 1     chr1        1  5666667 0.4705710
#> 2     chr1  5666667 11333334 0.2352942
#> 3     chr1 11333334 17000001 0.3529413