nearest-methods function

Find the nearest range neighbors for ChromatinAssay objects

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

## 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