Documentation for SLiM function setHotspotMap, 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.
setHotspotMap(multipliers, ends, sex)An object of type numeric. See details for description.
An object of type null or integer. The default value is NULL.
See details for description.
An object of type string. Must be of length 1 (a singleton). The
default value is "*". See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 662.
In nucleotide-based models, set the mutation rate multiplier along the chromosome. There are two ways to call this method. If the optional ends parameter is NULL (the default), then multipliers must be a singleton value that specifies a single multiplier to be used along the entire chromosome. If, on the other hand, ends is supplied, then multipliers and ends must be the same length, and the values in ends must be specified in ascending order. In that case, multipliers and ends taken together specify the multipliers to be used along successive contiguous stretches of the chromosome, from beginning to end; the last position specified in ends should extend to the end of the chromosome (as previously determined, during simulation initialization). See the initializeHotspotMap() function for further discussion of precisely how these multipliers and positions are interpreted. If the optional sex parameter is "*" (the default), then the supplied hotspot map will be used for both sexes (which is the only option for hermaphroditic simulations). In sexual simulations sex may be "M" or "F" instead, in which case the supplied hotspot map is used only for that sex. Note that whether sex-specific hotspot maps will be used is set by the way that the simulation is initially configured with initializeHotspot(), and cannot be changed with this method; so if the simulation was set up to use sex-specific hotspot maps then sex must be "M" or "F" here, whereas if it was set up not to, then sex must be "*" or unsupplied here. If a simulation needs sex-specific hotspot maps only some of the time, the male and female maps can simply be set to be identical the rest of the time. The hotspot map is normally constant in simulations, so be sure you know what you are doing.
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(),
drawBreakpoints(),
setAncestralNucleotides(),
setGeneConversion(),
setMutationRate(),
setRecombinationRate()