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

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function setAncestralNucleotides, 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.

1	setAncestralNucleotides(sequence)

sequence

An object of type integer or string. See details for description.

This method, which may be called only in nucleotide-based models (see section 1.8), replaces the ancestral nucleotide sequence for the model. The sequence parameter is interpreted exactly as it is in the initializeAncestralSequence() function; see that documentation for details (section 23.1). The length of the ancestral sequence is returned. It is unusual to replace the ancestral sequence in a running simulation, since the nucleotide states of segregating and fixed mutations will depend upon the original ancestral sequence. It can be useful when loading a new population state with readFromMS() or readFromVCF(), such as when resetting the simulation state to an earlier state in a conditional simulation; however, that is more commonly done using readFromPopulationFile() with a SLiM or .trees file.

An object of type integer. Return will be of length 1 (a singleton)

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.