intervals (version 0.15.1)

intervals-package: Tools for working with points and intervals

Description

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

Arguments

Acknowledgments

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

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.

See Also

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