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

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function initializeAncestralNucleotides, 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.

1	initializeAncestralNucleotides(sequence)

sequence

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

This function, which may be called only in nucleotide-based models (see section 1.8), supplies an ancestral nucleotide sequence for the model. The sequence parameter may be an integer vector providing nucleotide values (A=0, C=1, G=2, T=3), or a string vector providing single-character nucleotides ("A", "C", "G", "T"), or a singleton string providing the sequence as one string ("ACGT..."), or a singleton string providing the filesystem path of a FASTA file which will be read in to provide the sequence (if the file contains than one sequence, the first sequence will be used). Only A/C/G/T nucleotide values may be provided; other symbols, such as those for amino acids, gaps, or nucleotides of uncertain identity, are not allowed. The two semantic meanings of sequence that involve a singleton string value are distinguished heuristically; a singleton string that contains only the letters ACGT will be assumed to be a nucleotide sequence rather than a filename. The length of the ancestral sequence is returned. A utility function, randomNucleotides(), is provided by SLiM to assist in generating simple random nucleotide sequences; see section 23.15.1.

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.