join_overlap_intersect {plyranges} | R Documentation

## Join by overlapping Ranges

### Description

Join by overlapping Ranges

### Usage

    join_overlap_intersect(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

    join_overlap_intersect_within(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

    join_overlap_intersect_directed(
      x,
      y,
      maxgap,
      minoverlap,
      suffix = c(".x", ".y")
    )

    join_overlap_intersect_within_directed(
      x,
      y,
      maxgap,
      minoverlap,
      suffix = c(".x", ".y")
    )

    join_overlap_inner(x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y"))

    join_overlap_inner_within(
      x,
      y,
      maxgap = -1L,
      minoverlap = 0L,
      suffix = c(".x", ".y")
    )

    join_overlap_inner_directed(
      x,
      y,
      maxgap = -1L,
      minoverlap = 0L,
      suffix = c(".x", ".y")
    )

    join_overlap_inner_within_directed(
      x,
      y,
      maxgap = -1L,
      minoverlap = 0L,
      suffix = c(".x", ".y")
    )

    join_overlap_left(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

    join_overlap_left_within(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

    join_overlap_left_directed(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))

    join_overlap_left_within_directed(
      x,
      y,
      maxgap,
      minoverlap,
      suffix = c(".x", ".y")
    )

### 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.
`suffix` | Character to vectors to append to common columns in x and y (default = `c(".x", ".y")`).

### Details

The function `join_overlap_intersect()` finds the genomic intervals that are the overlapping ranges between x and y and returns a new ranges object with metadata columns from x and y.

The function `join_overlap_inner()` is equivalent to `find_overlaps()`.

The function `join_overlap_left()` performs a left outer join between x and y. It returns all ranges in x that overlap or do not overlap ranges in y plus metadata columns common to both. If there is no overlapping range the metadata column will contain a missing value.

The function `join_overlap_self()` find all overlaps between a ranges object x and itself.

All of these functions have two suffixes that modify their behavior. The `within` suffix, returns only ranges in x that are completely overlapped within in y. The `directed` suffix accounts for the strandedness of the ranges when performing overlaps.

### Value

a GRanges object

### See Also

`join_overlap_self()`, `join_overlap_left()`, `find_overlaps()`

### Examples

    x <- as_iranges(data.frame(start = c(11, 101), end = c(21, 201)))
    y <- as_iranges(data.frame(start = c(10, 20, 50, 100, 1),
                               end = c(19, 21, 105, 202, 5)))

    # self
    join_overlap_self(y)

    # intersect takes common interval
    join_overlap_intersect(x,y)

    # within
    join_overlap_intersect_within(x,y)

    # left, and inner join, it's often useful having an id column here
    y <- y %>% mutate(id = 1:n())
    x <- x %>% mutate(id = 1:n())
    join_overlap_inner(x,y)
    join_overlap_left(y,x, suffix = c(".left", ".right"))

[Package plyranges version 1.12.1 Index]