count_overlaps {plyranges} | R Documentation

## Count the number of overlaps between two Ranges objects

### Description

Count the number of overlaps between two Ranges objects

### Usage

    count_overlaps(x, y, maxgap, minoverlap)

    ## S3 method for class 'IntegerRanges'
    count_overlaps(x, y, maxgap = -1L, minoverlap = 0L)

    ## S3 method for class 'GenomicRanges'
    count_overlaps(x, y, maxgap = -1L, minoverlap = 0L)

    count_overlaps_within(x, y, maxgap, minoverlap)

    ## S3 method for class 'IntegerRanges'
    count_overlaps_within(x, y, maxgap = 0L, minoverlap = 1L)

    ## S3 method for class 'GenomicRanges'
    count_overlaps_within(x, y, maxgap = 0L, minoverlap = 1L)

    count_overlaps_directed(x, y, maxgap, minoverlap)

    ## S3 method for class 'GenomicRanges'
    count_overlaps_directed(x, y, maxgap = -1L, minoverlap = 0L)

    count_overlaps_within_directed(x, y, maxgap, minoverlap)

    ## S3 method for class 'GenomicRanges'
    count_overlaps_within_directed(x, y, maxgap = -1L, minoverlap = 0L)

### Arguments

`x, y` | Objects representing ranges
`maxgap, minoverlap` | The maximimum gap between intervals as an integer greater than or equal to zero. The minimum amount of overlap between intervals as an integer greater than zero, accounting for the maximum gap.

### Value

An integer vector of same length as x.

### Examples

    query <- data.frame(start = c(5,10, 15,20), width = 5, gc = runif(4)) %>%
                 as_iranges()
    subject <- data.frame(start = 2:6, width = 3:7, label = letters[1:5]) %>%
                 as_iranges()
    query %>% mutate(n_olap = count_overlaps(., subject),
                     n_olap_within = count_overlaps_within(., subject))

[Package plyranges version 1.12.1 Index]