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

In timoast/signac: Analysis of Single-Cell Chromatin Data

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,Seurat'
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)

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

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

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

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

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

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

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

## S4 method for signature 'Seurat,Seurat'
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, ...)

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

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

## S4 method for signature 'Seurat,Seurat'
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

Functions

• precede(x = ChromatinAssay, subject = ANY): method for ChromatinAssay, ANY

• precede(x = ChromatinAssay, subject = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• precede(x = ANY, subject = Seurat): method for ANY, Seurat

• precede(x = Seurat, subject = ANY): method for Seurat, ANY

• precede(x = Seurat, subject = Seurat): method for Seurat, Seurat

• follow(x = ANY, subject = ChromatinAssay): method for ANY, ChromatinAssay

• follow(x = ChromatinAssay, subject = ANY): method for ChromatinAssay, ANY

• follow(x = ChromatinAssay, subject = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• follow(x = ANY, subject = Seurat): method for ANY, Seurat

• follow(x = Seurat, subject = ANY): method for Seurat, ANY

• follow(x = Seurat, subject = Seurat): method for Seurat, Seurat

• nearest(x = ANY, subject = ChromatinAssay): method for ANY, ChromatinAssay

• nearest(x = ChromatinAssay, subject = ANY): method for ChromatinAssay, ANY

• nearest(x = ChromatinAssay, subject = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• nearest(x = ANY, subject = Seurat): method for ANY, Seurat

• nearest(x = Seurat, subject = ANY): method for Seurat, ANY

• nearest(x = Seurat, subject = Seurat): method for Seurat, Seurat

• distance(x = ANY, y = ChromatinAssay): method for ANY, ChromatinAssay

• distance(x = ChromatinAssay, y = ANY): method for ChromatinAssay, ANY

• distance(x = ChromatinAssay, y = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• distance(x = ANY, y = Seurat): method for ANY, Seurat

• distance(x = Seurat, y = ANY): method for Seurat, ANY

• distance(x = Seurat, y = Seurat): method for Seurat, Seurat

• distanceToNearest(x = ANY, subject = ChromatinAssay): method for ANY, ChromatinAssay

• distanceToNearest(x = ChromatinAssay, subject = ANY): method for ChromatinAssay, ANY

• distanceToNearest(x = ChromatinAssay, subject = ChromatinAssay): method for ChromatinAssay, ChromatinAssay

• distanceToNearest(x = ANY, subject = Seurat): method for ANY, Seurat

• distanceToNearest(x = Seurat, subject = ANY): method for Seurat, ANY

• distanceToNearest(x = Seurat, subject = Seurat): method for Seurat, Seurat

See Also

• nearest-methods in the IRanges package.

• nearest-methods in the GenomicRanges package

• ChromatinAssay-class

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.