initializeGeneConversion: SLiM method initializeGeneConversion
In rdinnager/slimrlang: Write SLiM Population Genetics Simulation Scripts in R

Description Usage Arguments Details Value Copyright Author(s)

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
)

`nonCrossoverFraction`	An object of type numeric or numeric or numeric or numeric. Must be of length 1 (a singleton). See details for description.
`meanLength`	An object of type numeric or numeric or numeric or numeric. Must be of length 1 (a singleton). See details for description.
`simpleConversionFraction`	An object of type numeric or numeric or numeric or numeric. Must be of length 1 (a singleton). See details for description.
`bias`	An object of type numeric or numeric or numeric or numeric. Must be of length 1 (a singleton). The default value is `0`. See details for description.

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.

An object of type void.

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/

Benjamin C Haller (bhaller@benhaller.com) and Philipp W Messer (messer@cornell.edu)

rdinnager/slimrlang documentation built on June 20, 2020, 8:17 p.m.