07-breakpoints: Class '"Breakpoints"'

In SVAlignR: Recovering Structure of Long Molecules from Structural Variation Data

Class "Breakpoints"

Description

Classes for working with collections of breakpoints.

Usage

Breakpoints(working)
## S4 method for signature 'Breakpoints,missing'
plot(x, y, colset, ...)

Arguments

working	A data frame containing the locations of break points. These should be seven consecutive columns, starting with the break point id followed by three columns each (chromosome, start, stop) for each side of the break point.
x	An object of the Breakpoints class.
y	Anything; it is ignored.
colset	A character vector of color specifications.
...	Extra graphical parameters.

Value

The Breakpoints constructor returna a newly created object of the Breakpoints class. The plot method invisible returns its first argument.

Objects from the Class

Objects should be defined using the Breakpoints constructor. You typically pass in a data frame containing columns with the name/id of the breakpoint, and their chromosome name, start, and stop positions for each side of the break.

Slots

relLocation:

A numeric vector giving relative coordinates (in the unit interval) of the breakpoints along a chromosome, with first and last break points mapped to 0 and 1.

labels:

A character vector containing the names of the chromosomes.

ypos:

A numeric vector indicating the chromosomes involved in the full set of break points.

spread:

How far the display of different chromosomes should be spread apart on the y-axis.

id:

The character vector of break point names.

Author(s)

Kevin R. Coombes <[e-mail]>

SVAlignR documentation built on Sept. 4, 2025, 3:01 p.m.