nearest-methods: Find the nearest range neighbors for ChromatinAssay objects

In Honchkrow/SignacSlim: The slim version of signac

Find the nearest range neighbors for ChromatinAssay objects

Description

The precede, follow, nearest, distance, distanceToNearest methods are available for ChromatinAssay objects.

Usage

## S4 method for signature 'ANY,ChromatinAssay'
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ChromatinAssay,ANY'
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ANY,ChromatinAssay'
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ChromatinAssay,ANY'
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ANY,ChromatinAssay'
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ChromatinAssay,ANY'
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

## S4 method for signature 'ANY,ChromatinAssay'
distance(x, y, ignore.strand = FALSE, ...)

## S4 method for signature 'ChromatinAssay,ANY'
distance(x, y, ignore.strand = FALSE, ...)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
distance(x, y, ignore.strand = FALSE, ...)

## S4 method for signature 'ANY,ChromatinAssay'
distanceToNearest(x, subject, ignore.strand = FALSE, ...)

## S4 method for signature 'ChromatinAssay,ANY'
distanceToNearest(x, subject, ignore.strand = FALSE, ...)

## S4 method for signature 'ChromatinAssay,ChromatinAssay'
distanceToNearest(x, subject, ignore.strand = FALSE, ...)

Arguments

x	A query ChromatinAssay object
subject	The subject GRanges or ChromatinAssay object. If missing, x is used as the subject.
select	Logic for handling ties. See nearest-methods in the GenomicRanges package.
ignore.strand	Logical argument controlling whether strand information should be ignored.
y	For the distance method, a GRanges object or a ChromatinAssay object
...	Additional arguments for methods

Value

nearest range neighbors

Functions

• precede,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY

• precede,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay

• follow,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay

• follow,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY

• follow,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay

• nearest,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay

• nearest,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY

• nearest,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay

• distance,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay

• distance,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY

• distance,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay

• distanceToNearest,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay

• distanceToNearest,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY

• distanceToNearest,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay

See Also

• nearest-methods in the IRanges package.

• nearest-methods in the GenomicRanges package

• ChromatinAssay-class

Examples

print("see https://satijalab.org/signac/reference/chromatinassay-class")

Honchkrow/SignacSlim documentation built on April 9, 2022, 1:49 a.m.