Signac: nearest-methods – R documentation

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Signac

nearest-methods

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,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY
precede,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
precede,ANY,Seurat-method: method for ANY, Seurat
precede,Seurat,ANY-method: method for Seurat, ANY
precede,Seurat,Seurat-method: method for Seurat, Seurat
follow,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay
follow,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY
follow,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
follow,ANY,Seurat-method: method for ANY, Seurat
follow,Seurat,ANY-method: method for Seurat, ANY
follow,Seurat,Seurat-method: method for Seurat, Seurat
nearest,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay
nearest,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY
nearest,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
nearest,ANY,Seurat-method: method for ANY, Seurat
nearest,Seurat,ANY-method: method for Seurat, ANY
nearest,Seurat,Seurat-method: method for Seurat, Seurat
distance,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay
distance,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY
distance,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
distance,ANY,Seurat-method: method for ANY, Seurat
distance,Seurat,ANY-method: method for Seurat, ANY
distance,Seurat,Seurat-method: method for Seurat, Seurat
distanceToNearest,ANY,ChromatinAssay-method: method for ANY, ChromatinAssay
distanceToNearest,ChromatinAssay,ANY-method: method for ChromatinAssay, ANY
distanceToNearest,ChromatinAssay,ChromatinAssay-method: method for ChromatinAssay, ChromatinAssay
distanceToNearest,ANY,Seurat-method: method for ANY, Seurat
distanceToNearest,Seurat,ANY-method: method for Seurat, ANY
distanceToNearest,Seurat,Seurat-method: method for Seurat, Seurat