Documentation for SLiM function initializeGeneConversion, 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.
initializeGeneConversion(
nonCrossoverFraction,
meanLength,
simpleConversionFraction,
bias,
redrawLengthsOnFailure
)An object of type numeric or numeric or numeric or numeric or logical. Must be of length 1 (a singleton). See details for description.
An object of type numeric or numeric or numeric or numeric or logical. Must be of length 1 (a singleton). See details for description.
An object of type numeric or numeric or numeric or numeric or logical. Must be of length 1 (a singleton). See details for description.
An object of type numeric or numeric or numeric or numeric or
logical. Must be of length 1 (a singleton). The default value is 0. See
details for description.
An object of type numeric or numeric or numeric
or numeric or logical. Must be of length 1 (a singleton). The default value is
F. See details for description.
An object of type void.
Documentation for this function can be found in the official SLiM manual: page 647.
Calling this function switches the recombination model from a "simple crossover" model to a "double-stranded break (DSB)" model, and configures the details of the gene conversion tracts that will therefore be modeled (see section 1.5.6 for discussion of these models). The fraction of DSBs that will be modeled as non-crossover events is given by nonCrossoverFraction. The mean length of gene conversion tracts (whether associated with crossover or non-crossover events) is given by meanLength; the actual extent of a gene conversion tract will be the sum of two independent draws from a geometric distribution with mean meanLength/2. The fraction of gene conversion tracts that are modeled as "simple" is given by simpleConversionFraction; the remainder will be modeled as "complex", involving repair of heteroduplex mismatches. Finally, the GC bias during heteroduplex mismatch repair is given by bias, with the default of 0.0 indicating no bias, 1.0 indicating an absolute preference for G/C mutations over A/T mutations, and -1.0 indicating an absolute preference for A/T mutations over G/C mutations. A non-zero bias may only be set in nucleotide-based models (see section 1.8). This function, and the way that gene conversion is modeled, fundamentally changed in SLiM 3.3; see section 1.5.6 for discussion. Beginning in SLiM 4.1, the redrawLengthsOnFailure parameter can be used to modify the internal mechanics of layout of gene conversion tracts. If it is F (the default, and the only behavior supported before SLiM 4.1), then if an attempt to lay out gene conversion tracts fails (because the tracts overlap each other, or overlap the start or end of the chromosome), SLiM will try again by drawing new positions for the tracts - essentially shuffling the tracts around to try to find positions for them that don't overlap. If redrawLengthsOnFailure is T, then if an attempt to lay out gene conversion tracts fails, SLiM will try again by drawing new lengths for the tracts, as well as new positions. This makes it more likely that layout will succeed, but risks biasing the realized mean tract length downward from the requested mean length (since layout of long tracts is more likely fail due to overlap). In either case, if SLiM attempts to lay out gene conversion tracts 100 times without success, an error will result. That error indicates that the specified constraints for gene conversion are difficult to satisfy - tracts may commonly be so long that it is difficult or impossible to find an acceptable layout for them within the specified chromosome length. Setting redrawLengthsOnFailure to T may mitigate this problem, at the price of biasing the mean tract length downward as discussed.
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(),
initializeGenomicElementType(),
initializeGenomicElement(),
initializeHotspotMap(),
initializeInteractionType(),
initializeMutationRate(),
initializeMutationTypeNuc(),
initializeMutationType(),
initializeRecombinationRate(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeGeneConversion()