genomicDensity: Calculate genomic region density

In circlize: Circular Visualization

Calculate genomic region density

Description

Calculate genomic region density

Usage

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))
head(genomicDensity(bed, count_by = "number"))

circlize documentation built on May 29, 2024, 1:59 a.m.