R: Calculate genomic region density

genomicDensity {circlize} | R Documentation

## Calculate genomic region density

### Description

Calculate genomic region density

### Usage

    genomicDensity(region, window.size = 1e7, n.window = NULL, overlap = TRUE, 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
`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 percent of overlapping. And if the input is a bed-format data frame, there will be an additionally chromosome name column.

### References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

### Examples

    bed = generateRandomBed()
    bed = subset(bed, chr == "chr1")
    head(genomicDensity(bed))

[Package circlize version 0.4.5 Index]