Documentation for SLiM function initializeMutationRate, which is a method
of the SLiM class Initialize.
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.
initializeMutationRate(rates, 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 651.
Set the mutation rate per base position per gamete. To be precise, this mutation rate is the expected mean number of mutations that will occur per base position per gamete; note that this is different from how the recombination rate is defined (see initializeRecombinationRate()). The number of mutations that actually occurs at a given base position when generating an offspring genome is, in effect, drawn from a Poisson distribution with that expected mean (but under the hood SLiM uses a mathematically equivalent but much more efficient strategy). It is possible for this Poisson draw to indicate that two or more new mutations have arisen at the same base position, particularly when the mutation rate is very high; in this case, the new mutations will be added to the site one at a time, and as always the mutation stacking policy (see section 1.5.3) will be followed. There are two ways to call this function. If the optional ends parameter is NULL (the default), then rates must be a singleton value that specifies a single mutation rate to be used along the entire chromosome. If, on the other hand, ends is supplied, then rates and ends must be the same length, and the values in ends must be specified in ascending order. In that case, rates and ends taken together specify the mutation rates 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 (i.e. at least to the end of the last genomic element, if not further). For example, if the following call is made: initializeMutationRate(c(1e-7, 2.5e-8), c(5000, 9999)); then the result is that the mutation rate for bases 0...5000 (inclusive) will be 1e-7, and the rate for bases 5001...9999 (inclusive) will be 2.5e-8. Note that mutations are generated by SLiM only within genomic elements, regardless of the mutation rate map. In effect, the mutation rate map given is intersected with the coverage area of the genomic elements defined; areas outside of any genomic element are given a mutation rate of zero. There is no harm in supplying a mutation rate map that specifies rates for areas outside of the genomic elements defined; that rate information is simply not used. The overallMutationRate family of properties on Chromosome provide the overall mutation rate after genomic element coverage has been taken into account, so it will reflect the rate at which new mutations will actually be generated in the simulation as configured. If the optional sex parameter is "*" (the default), then the supplied mutation rate 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 mutation rate map is used only for that sex (i.e., when generating a gamete from a parent of that sex). In this case, two calls must be made to initializeMutationRate(), one for each sex, even if a rate of zero is desired for the other sex; no default mutation rate map is supplied. In nucleotide-based models, initializeMutationRate() may not be called. Instead, the desired sequence-based mutation rate(s) should be expressed in the mutationMatrix parameter to initializeGenomicElementType(). If variation in the mutation rate along the chromosome is desired, initializeHotspotMap() should be used.
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 Initialize:
Init,
initializeAncestralNucleotides(),
initializeGeneConversion(),
initializeGenomicElementType(),
initializeGenomicElement(),
initializeHotspotMap(),
initializeInteractionType(),
initializeMutationTypeNuc(),
initializeMutationType(),
initializeRecombinationRate(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeMutationRate()