ContactMatrix-distances: Compute linear distances from ContactMatrix objects

In InteractionSet: Base Classes for Storing Genomic Interaction Data

Description

Methods to compute linear distances between pairs of interacting regions in a ContactMatrix object.

Usage

## S4 method for signature 'ContactMatrix'
pairdist(x, type="mid")

## S4 method for signature 'ContactMatrix'
intrachr(x)

Arguments

x	A ContactMatrix object.
type	A character string specifying the type of distance to compute. See ?pairdist,InteractionSet-method for possible values.

Details

pairdist,ContactMatrix-method will return a matrix of integer (or, if type="intra", logical) values. Each entry of this matrix specifies the distance between the interacting loci that are represented by the corresponding row and column. If type="intra", each entry indicates whether the corresponding interaction is intra-chromosomal. Running intrachr(x) is equivalent to pairdist(x, type="intra") for any ContactMatrix object x. See pairdist,InteractionSet-method for more details on the type of distances that can be computed.

Value

An integer or logical matrix of the same dimensions as x, containing the specified distances.

Author(s)

Aaron Lun

See Also

ContactMatrix-class, pairdist,InteractionSet-method

Examples

example(ContactMatrix, echo=FALSE)

pairdist(x)
pairdist(x, type="gap")
pairdist(x, type="span")
pairdist(x, type="diag")

intrachr(x)

InteractionSet documentation built on April 17, 2021, 6 p.m.