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

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function nucleotides, which is a method of the SLiM class Genome. 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	nucleotides(start, end, format)

`start`	An object of type null or integer. Must be of length 1 (a singleton). The default value is `NULL`. See details for description.
`end`	An object of type null or integer. Must be of length 1 (a singleton). The default value is `NULL`. See details for description.
`format`	An object of type string. Must be of length 1 (a singleton). The default value is `"string"`. See details for description.

Returns the nucleotide sequence for the genome. This is the current ancestral sequence, as would be returned by the Chromosome method ancestralNucleotides(), with the nucleotides for any nucleotide-based mutations in the genome overlaid. The range of the returned sequence may be constrained by a start position given in start and/or an end position given in end; nucleotides will be returned from start to end, inclusive. The default value of NULL for start and end represent the first and last base positions of the chromosome, respectively. The format of the returned sequence is controlled by the format parameter. A format of "string" will return the sequence as a singleton string (e.g., "TATA"). A format of "char" will return a string vector with one element per nucleotide (e.g., "T", "A", "T", "A"). A format of "integer" will return an integer vector with values A=0, C=1, G=2, T=3 (e.g., 3, 0, 3, 0). A format of "codon" will return an integer vector with values from 0 to 63, based upon successive nucleotide triplets in the sequence (which, for this format, must have a length that is a multiple of three); see the ancestralNucleotides() documentation for details. If the sequence returned is likely to be long, the "string" format will be the most memory-efficient, and may also be the fastest (but may be harder to work with). Several helper functions are provided for working with sequences, such as nucleotideCounts() to get the counts of A/C/G/ T nucleotides in a sequence, nucleotideFrequencies() to get the same information as frequencies, and codonsToAminoAcids() to convert a codon sequence (such as provided by the codon format described above) to an amino acid sequence; see section 23.15.1.

An object of type integer or string.

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.