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Signac (version 1.14.0)

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 ANY,ChromatinAssay
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ChromatinAssay,ANY
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ChromatinAssay,ChromatinAssay
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ANY,Seurat
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for Seurat,ANY
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for Seurat,Seurat
precede(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ANY,ChromatinAssay
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ChromatinAssay,ANY
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ChromatinAssay,ChromatinAssay
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ANY,Seurat
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for Seurat,ANY
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for Seurat,Seurat
follow(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ANY,ChromatinAssay
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ChromatinAssay,ANY
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ChromatinAssay,ChromatinAssay
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ANY,Seurat
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for Seurat,ANY
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for Seurat,Seurat
nearest(x, subject, select = c("arbitrary", "all"), ignore.strand = FALSE)
# S4 method for ANY,ChromatinAssay
distance(x, y, ignore.strand = FALSE, ...)
# S4 method for ChromatinAssay,ANY
distance(x, y, ignore.strand = FALSE, ...)
# S4 method for ChromatinAssay,ChromatinAssay
distance(x, y, ignore.strand = FALSE, ...)
# S4 method for ANY,Seurat
distance(x, y, ignore.strand = FALSE, ...)
# S4 method for Seurat,ANY
distance(x, y, ignore.strand = FALSE, ...)
# S4 method for Seurat,Seurat
distance(x, y, ignore.strand = FALSE, ...)
# S4 method for ANY,ChromatinAssay
distanceToNearest(x, subject, ignore.strand = FALSE, ...)
# S4 method for ChromatinAssay,ANY
distanceToNearest(x, subject, ignore.strand = FALSE, ...)
# S4 method for ChromatinAssay,ChromatinAssay
distanceToNearest(x, subject, ignore.strand = FALSE, ...)
# S4 method for ANY,Seurat
distanceToNearest(x, subject, ignore.strand = FALSE, ...)
# S4 method for Seurat,ANY
distanceToNearest(x, subject, ignore.strand = FALSE, ...)
# S4 method for 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