drawBreakpoints: SLiM method drawBreakpoints
In rdinnager/slimrlang: Write SLiM Population Genetics Simulation Scripts in R

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function drawBreakpoints, which is a method of the SLiM class Chromosome. Note that the R function is a stub, it does not do anything in R (except bring up this documentation). It will only do anything useful when used inside a slim_block function further nested in a slim_script function call, where it will be translated into valid SLiM code as part of a full SLiM script.

1	drawBreakpoints(parent, n)

`parent`	An object of type null or Individual object. Must be of length 1 (a singleton). The default value is `NULL`. See details for description.
`n`	An object of type null or integer. Must be of length 1 (a singleton). The default value is `NULL`. See details for description.

Draw recombination breakpoints, using the chromosome’s recombination rate map, the current gene conversion parameters, and (in some cases – see below) any active and applicable recombination() callbacks. The number of breakpoints to generate, n, may be supplied; if it is NULL (the default), the number of breakpoints will be drawn based upon the overall recombination rate and the chromosome length (following the standard procedure in SLiM). Note that if the double-stranded breaks model has been chosen, the number of breakpoints generated will probably not be equal to the number requested, because most breakpoints will entail gene conversion tracts, which entail additional crossover breakpoints. It is generally recommended that the parent individual be supplied to this method, but parent is NULL by default. The individual supplied in parent is used for two purposes. First, in sexual models that define separate recombination rate maps for males versus females, the sex of parent will be used to determine which map is used; in this case, a non-NULL value must be supplied for parent, since the choice of recombination rate map must be determined. Second, in models that define recombination() callbacks, parent is used to determine the various pseudo-parameters that are passed to recombination() callbacks (individual, genome1, genome2, subpop), and the subpopulation to which parent belongs is used to select which recombination() callbacks are applicable; given the necessity of this information, recombination() callbacks will not be called as a side effect of this method if parent is NULL. Apart from these two uses, parent is not used, and the caller does not guarantee that the generated breakpoints will actually be used to recombine the genomes of parent in particular.

An object of type integer.

This is documentation for a function in the SLiM software, and has been reproduced from the official manual, which can be found here: http://benhaller.com/slim/SLiM_Manual.pdf. This documentation is Copyright © 2016–2020 Philipp Messer. All rights reserved. More information about SLiM can be found on the official website: https://messerlab.org/slim/

Benjamin C Haller (bhaller@benhaller.com) and Philipp W Messer (messer@cornell.edu)

rdinnager/slimrlang documentation built on June 20, 2020, 8:17 p.m.