| 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.
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 0.13.1
Index]