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.
initializeAncestralNucleotides(sequence)An object of type integer or string. See details for description.
An object of type integer. Return will be of length 1 (a singleton)
Documentation for this function can be found in the official SLiM manual: page 647.
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 25.18.1.
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,
initializeGeneConversion(),
initializeGenomicElementType(),
initializeGenomicElement(),
initializeHotspotMap(),
initializeInteractionType(),
initializeMutationRate(),
initializeMutationTypeNuc(),
initializeMutationType(),
initializeRecombinationRate(),
initializeSLiMModelType(),
initializeSLiMOptions(),
initializeSex(),
initializeSpecies(),
initializeTreeSeq()
## This just brings up the documentation:
initializeAncestralNucleotides()