Documentation for SLiM function initializeHotspotMap, 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.
initializeHotspotMap(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 649.
In nucleotide-based models, set the mutation rate multiplier along the chromosome. Nucleotidebased models define sequence-based mutation rates that are set up with the mutationMatrix parameter to initializeGenomicElementType(). If no hotspot map is specified by calling initializeHotspotMap(), a hotspot map with a multiplier of 1.0 across the whole chromosome is assumed (and so the sequence-based rates are the absolute mutation rates used by SLiM). A hotspot * PA→C PA→G PA→T PC→A * PC→G PC→T PG→A PG→C * PG→T PT→A PT→C PT→G * * PAAA→ACA PAAA→AGA PAAA→ATA * PAAC→ACC PAAC→AGC PAAC→ATC * PAAG→ACG PAAG→AGG PAAG→ATG * PAAT→ACT PAAT→AGT PAAT→ATT PACA→AAA * PACA→AGA PACA→ATA PACC→AAC * PACC→AGC PACC→ATC PACG→AAG * PACG→AGG PACG→ATG . . . . . . . . . . . . PTTC→TAC PTTC→TCC PTTC→TGC * PTTG→TAG PTTG→TCG PTTG→TGG * PTTT→TAT PTTT→TCT PTTT→TGT * map modifies the sequence-based rates by scaling them up in some regions, with multipliers greater than 1.0 (representing mutational hot spots), and/or scaling them down in some regions, with multipliers less than 1.0 (representing mutational cold spots). There are two ways to call this function. 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 (typically 1.0, but not required to be). 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 (i.e. at least to the end of the last genomic element, if not further). For example, if the following call is made: initializeHotspotMap(c(1.0, 1.2), c(5000, 9999)); then the result is that the mutation rate multiplier for bases 0...5000 (inclusive) will be 1.0 (and so the specified sequence-based mutation rates will be used verbatim), and the multiplier for bases 5001...9999 (inclusive) will be 1.2 (and so the sequence-based mutation rates will be multiplied by 1.2 within the region). Note that mutations are generated by SLiM only within genomic elements, regardless of the hotspot map. In effect, the hotspot map given is intersected with the coverage area of the genomic elements defined; areas outside of any genomic element are given a multiplier of zero. There is no harm in supplying a hotspot map that specifies multipliers for areas outside of the genomic elements defined; the excess information is simply not used. 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 (i.e., when generating a gamete from a parent of that sex). In this case, two calls must be made to initializeHotspotMap(), one for each sex, even if a multiplier of 1.0 is desired for the other sex; no default hotspot map is supplied.
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(),
initializeInteractionType(),
initializeMutationRate(),
initializeMutationTypeNuc(),
initializeMutationType(),
initializeRecombinationRate(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeHotspotMap()