InteractionSet (version 1.0.4)

ContactMatrix distances: Compute linear distances from ContactMatrix objects

Description

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

Usage

"pairdist"(x, type="mid")
"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.

Value

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

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.

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)