join_overlap_self {plyranges} | R Documentation

## Find overlaps within a Ranges object

### Description

Find overlaps within a Ranges object

### Usage

    join_overlap_self(x, maxgap, minoverlap)

    join_overlap_self_within(x, maxgap, minoverlap)

    join_overlap_self_directed(x, maxgap, minoverlap)

    join_overlap_self_within_directed(x, maxgap, minoverlap)

### Arguments

`x` | A Ranges object
`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.

### Details

Self overlaps find any overlaps (or overlaps within or overlaps directed) between a ranges object and itself.

### Value

a Ranges object

### See Also

`find_overlaps()`, `join_overlap_inner()`

### Examples

    query <- data.frame(start = c(5,10, 15,20), width = 5, gc = runif(4)) %>%
                 as_iranges()

    join_overlap_self(query)

    # -- GRanges objects, strand is ignored by default
    query  <- data.frame(seqnames = "chr1",
                   start = c(11,101),
                   end = c(21, 200),
                   name = c("a1", "a2"),
                   strand = c("+", "-"),
                   score = c(1,2)) %>%
               as_granges()

    # ignores strandedness
    join_overlap_self(query)
    join_overlap_self_within(query)
    # adding directed prefix includes strand
    join_overlap_self_directed(query)

[Package plyranges version 1.6.10 Index]