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Find the nearest range neighbors for GRangesAssay objects

Source: R/iranges-methods.R
nearest-methods.Rd

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

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arguments

x

A query GRangesAssay object

subject

The subject GenomicRanges::GRanges() or GRangesAssay object. If missing, x is used as the subject.

select

Logic for handling ties. See GenomicRanges::nearest-methods()

ignore.strand

Logical argument controlling whether strand information should be ignored.

y

For the distance method, a GenomicRanges::GRanges() object or a GRangesAssay object

...

Additional arguments for methods

Functions

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

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

  • 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 = GRangesAssay): method for ANY, GRangesAssay

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

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

  • 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 = GRangesAssay): method for ANY, GRangesAssay

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

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

  • 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 = GRangesAssay): method for ANY, GRangesAssay

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

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

  • 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 = GRangesAssay): method for ANY, GRangesAssay

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

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

  • 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