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

Description Usage Arguments Details Value Copyright Author(s)

Documentation for SLiM function readFromMS, 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	readFromMS(filePath, mutationType)

`filePath`	An object of type string. Must be of length 1 (a singleton). See details for description.
`mutationType`	An object of type integer or MutationType object. Must be of length 1 (a singleton). See details for description.

Read new mutations from the MS format file at filePath and add them to the target genomes. The number of target genomes must match the number of genomes represented in the MS file. To read into all of the genomes in a given subpopulation pN, simply call pN.genomes.readFromMS(), assuming the subpopulation’s size matches that of the MS file. A vector containing all of the mutations created by readFromMS() is returned. Each mutation is created at the position specified in the file, using the mutation type given by mutationType. Positions are expected to be in [0,1], and are scaled to the length of the chromosome by multiplying by the last valid base position of the chromosome (i.e., one less than the chromosome length). Selection coefficients are drawn from the mutation type. The population of origin for each mutation is set to -1, and the generation of origin is set to the current generation. In a nucleotidebased model, if mutationType is nucleotide-based, a random nucleotide different from the ancestral nucleotide at the position will be chosen with equal probability. The target genomes correspond, in order, to the call lines in the MS file. In sex-based models that simulate the X or Y chromosome, null genomes in the target vector will be skipped, and will not be used to correspond to any call line; however, care should be taken in this case that the lines in the MS file correspond to the target genomes in the manner desired.

An object of type Mutation object.

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.