RangesMatchingList-class {IRanges} | R Documentation

## List of Matchings between Ranges

### Description

The `RangesMatchingList` class stores a set of matchings, represented as `RangesMatching` objects, between the ranges in one `RangesList` object and the ranges in another.

### Details

Roughly the same set of utilities are provided for `RangesMatchingList` as for `RangesMatching`:

The `as.matrix` method coerces a `RangesMatchingList` in a similar way to `RangesMatching`, except a column is prepended that indicates which space (or element in the query `RangesList`) to which the row corresponds.

The `as.table` method flattens or unlists the list, counts the number of matchings for each query range and outputs the counts as a `table`, which has the same shape as from a single `RangesMathing`.

To transpose a `RangesMatchingList` `x`, so that the subject and query in each space are interchanged, call `t(x)`. This allows, for example, counting the number of subjects that matched using `as.table`.

To get the actual regions of intersection between the overlapping ranges, use the `ranges` accessor.

### Coercion

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

  `as.matrix(x)`: calls `as.matrix` on each `RangesMatching`, combines them row-wise and offsets the indices so that they are aligned with the result of calling `unlist` on the query and subject (as long as the names on each, if any, are in the same order).
  `as.table(x)`: counts the number of matchings for each query range in `x` and outputs the counts as a `table`, which is aligned with the result of calling `unlist` on the query.
  `t(x)`: Interchange the query and subject in each space of `x`, returns a transposed `RangesMatchingList`.

### Accessors

  `space(x)`: gets the character vector naming the space in the query `RangesList` for each match, or `NULL` if the query did not have any names.
  `ranges(x, query, subject)`: returns a `RangesList` holding the intersection of the ranges in the `RangesList` objects `query` and `subject`, which should be the same subject and query used to generate `x`. Eventually, we might store the query and subject inside `x`, in which case the arguments would be redundant.

### Note

This class is highly experimental. It has not been well tested and may disappear at any time.

### Author(s)

Michael Lawrence

### See Also

`overlap`, which generates an instance of this class.

[Package IRanges version 1.2.3 Index]