R: Tools for working with points and intervals

intervals-package {intervals} | R Documentation

## Tools for working with points and intervals

### Description

Tools for working with and comparing sets of points and intervals.

### Details

Index:

`Intervals-class`

  Classes `"Intervals"` and `"Intervals_full"`.

`Intervals_virtual-class`

  Class `"Intervals_virtual"`.

`Intervals_virtual_or_numeric-class`

  Class union `"Intervals_virtual_or_numeric"`.

`as.matrix`

  Coerce endpoints to a matrix.

`c`

  Concatenate different sets of intervals.

`close_intervals`

  Re-represent integer intervals with open or closed endpoints.

`closed`

  Accessor for `closed` slot: closure vector/matrix.

`clusters`

  Identify clusters in a collection of positions or intervals.

`contract`

  Contract sets.

`distance_to_nearest`

  Compute distance to nearest position in a set of intervals.

`empty`

  Identify empty interval rows.

`expand`

  Expand sets.

`interval_complement`

  Compute the complement of a set of intervals.

`interval_difference`

  Compute set difference.

`interval_included`

  Assess inclusion of one set of intervals with respect to another.

`interval_intersection`

  Compute the intersection of one or more sets of intervals.

`interval_overlap`

  Assess which query intervals overlap which targets.

`interval_union`

  Compute the union of intervals in one or more interval matrices.

`is.na`

  Identify interval rows with `NA` endpoints.

`plot`

  S3 plotting methods for intervals objects.

`reduce`

  Compactly re-represent the points in a set of intervals.

`sgd`

  Yeast gene model sample data.

`size`

  Compute interval sizes.

`split`

  Split an intervals object according to a factor.

`type`

  Accessor for `type` slot: Z or R.

`which_nearest`

  Identify nearest member(s) in a set of intervals.

Further information is available in the following vignettes:

`intervals_overview`

  Overview of the intervals package.

### Acknowledgments

Thanks to Julien Gagneur, Simon Anders, and Wolfgang Huber for numerous helpful suggestions about the package content and code.

### Author(s)

Richard Bourgon <bourgon@ebi.ac.uk>

### See Also

See the genomeIntervals package in Bioconductor, which extends the functionality of this package.

[Package intervals version 0.15.2 Index]