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".
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_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.
reduce
Compactly re-represent the points in a set of intervals.
sgd
Yeast gene model sample data.
size
Compute interval sizes.
type
Accessor for type slot: Z or R.

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 0.10.3 Index]