# ranges-count-overlaps: Count the number of overlaps between two Ranges objects In plyranges: A fluent interface for manipulating GenomicRanges

## Description

Count the number of overlaps between two Ranges objects

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25``` ```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

 ```1 2 3 4 5 6``` ```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)) ```

plyranges documentation built on Nov. 8, 2020, 7:36 p.m.