Calculate genomic region density

genomicDensity(
    region,
    window.size = 1e7,
    n.window = NULL,
    overlap = TRUE,
    count_by = c("percent", "number"),
    chr.len = NULL)

Arguments

region	Genomic positions. It can be a data frame with two columns which are start positions and end positions on a single chromosome. It can also be a bed-format data frame which contains the chromosome column.
window.size	Window size to calculate genomic density
n.window	number of windows, if it is specified, `window.size` is ignored
overlap	Whether two neighbouring windows have half overlap
count_by	How to count the value for each window, `percent`: percent of the window covered by the input regions; `number`: number of regions that overlap to the window.
chr.len	the chromosome length. The value should be named vector

Details

It calculate the percent of each genomic windows that is covered by the input regions.

Value

If the input is a two-column data frame, the function returns a data frame with three columns: start position, end position and the overlapping (value depends on the count_by argument). And if the input is a bed-format data frame, there will be an additionally chromosome name column.

Examples

bed = generateRandomBed()
bed = subset(bed, chr == "chr1")
head(genomicDensity(bed))
#>    chr    start      end     value
#> 1 chr1        1 10000000 0.5174489
#> 2 chr1  5000001 15000000 0.5550511
#> 3 chr1 10000001 20000000 0.5354743
#> 4 chr1 15000001 25000000 0.5258289
#> 5 chr1 20000001 30000000 0.4530591
#> 6 chr1 25000001 35000000 0.5215807
head(genomicDensity(bed, count_by = "number"))
#>    chr    start      end value
#> 1 chr1        1 10000000    22
#> 2 chr1  5000001 15000000    28
#> 3 chr1 10000001 20000000    36
#> 4 chr1 15000001 25000000    36
#> 5 chr1 20000001 30000000    35
#> 6 chr1 25000001 35000000    32