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.
drawBreakpoints(parent, n)An object of type null or Individual object. Must be of length 1
(a singleton). The default value is NULL. See details for description.
An object of type null or integer. Must be of length 1 (a singleton).
The default value is NULL. See details for description.
An object of type integer.
Documentation for this function can be found in the official SLiM manual: page 662.
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. If a recombination() callback is called, genome1 for that callback will always be parent.genome1; in other words, drawBreakpoints() will always treat parent.genome1 as the initial copy strand. If the caller wishes to randomly choose an initial copy strand (which is usually desirable), they should do that themselves.
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/
Other Chromosome:
Chromosome,
ancestralNucleotides(),
setAncestralNucleotides(),
setGeneConversion(),
setHotspotMap(),
setMutationRate(),
setRecombinationRate()