Find the nearest range neighbors for ChromatinAssay objects

Source: R/iranges-methods.R

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

# 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,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

See also