# intervals-package {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.

### See Also

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

Documentation reproduced from package intervals, version 0.15.1. License: Artistic-2.0