Pairs-class {S4Vectors} | R Documentation

## Pairs objects

### Description

`Pairs` is a `Vector` that stores two parallel vectors (any object that can be a column in a `DataFrame`). It provides conveniences for performing binary operations on the vectors, as well as for converting between an equivalent list representation. Virtually all of the typical R vector operations should behave as expected.

A typical use case is representing the pairing from a `findOverlaps` call, for which `findOverlapPairs` is a shortcut.

### Constructor

  `Pairs(first, second, ..., names = NULL, hits = NULL)`: Constructs a Pairs object by aligning the vectors `first` and `second`. The vectors must have the same length, unless `hits` is specified. Arguments in `...` are combined as columns in the `mcols` of the result. The `names` argument specifies the names on the result. If `hits` is not `NULL`, it should be a `Hits` object that collates the elements in `first` and `second` to produce the corresponding pairs.

### Accessors

In the code snippets below, `x` is a `Pairs` object.

  `names(x)`, `names(x) <- value`: get or set the names

  `first(x)`, `first(x) <- value`: get or set the first member of each pair

  `second(x)`, `second(x) <- value`: get or set the second member of each pair

### Coercion

  `zipup(x)`: Interleaves the `Pairs` object `x` into a list, where each element is composed of a pair. The type of list depends on the type of the elements.

  `zipdown(x)`: The inverse of `zipup()`. Converts `x`, a list where every element is of length 2, to a `Pairs` object, by assuming that each element of the list represents a pair.

### Subsetting

In the code snippets below, `x` is a `Pairs` object.

  `x[i]`: Subset the Pairs object.

### Author(s)

Michael Lawrence

### See Also

- Hits-class, a typical way to define a pairing.

- `findOverlapPairs` in the IRanges package, which generates an instance of this class based on overlaps.

- setops-methods in the IRanges package, for set operations on Pairs objects.

### Examples

    p <- Pairs(1:10, Rle(1L, 10), score=rnorm(10), names=letters[1:10])
    identical(first(p), 1:10)
    mcols(p)$score
    p
    as.data.frame(p)
    z <- zipup(p)
    first(p) <- Rle(1:10)
    identical(zipdown(z), p)

[Package S4Vectors version 0.18.3 Index]