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

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.

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

Richard Bourgon <bourgon@ebi.ac.uk>

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

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.