Documentation for Mutation class from SLiM
This class represents a single point mutation. Mutations can be shared by the genomes of many individuals; if they reach fixation, they are converted to Substitution objects. Although Mutation has a tag property, like most SLiM classes, the subpopID can also store custom values if you don't need to track the origin subpopulation of mutations (see below). Section 1.5.2 presents an overview of the conceptual role of this class. This class has the following methods (functions):
This class has the following properties:
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The identifier for this mutation. Each mutation created during a run receives an immutable identifier that will be unique across the duration of the run. These identifiers are not re-used during a run, except that if a population file is loaded from disk, the loaded mutations will receive their original identifier values as saved in the population file.
A property of type logical. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: T if the mutation has fixed (in the SLiM sense of having been converted to a Substitution object), F otherwise. Since fixed/substituted mutations are removed from the simulation, you will only see this flag be T if you have held onto a mutation beyond its usual lifetime (see section 28.2).
A property of type logical. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: T if the mutation is segregating (in the SLiM sense of not having been either lost or converted to a Substitution object), F otherwise. Since both lost and fixed/substituted mutations are removed from the simulation, you will only see this flag be F if you have held onto a mutation beyond its usual lifetime (see section 28.2). Note that if isSegregating is F, isFixed will let you determine whether the mutation is no longer segregating because it was lost, or because it fixed.
A property of type MutationType object. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The MutationType from which this mutation was drawn.
A property of type string. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A string representing the nucleotide associated with this mutation; this will be "A", "C", "G", or "T". If the mutation is not nucleotide-based, this property is unavailable.
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: An integer representing the nucleotide associated with this mutation; this will be 0 (A), 1 (C), 2 (G), or 3 (T). If the mutation is not nucleotide-based, this property is unavailable.
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The tick in which this mutation arose.
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The position in the chromosome of this mutation.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The selection coefficient of the mutation, drawn from the distribution of fitness effects of its MutationType. If a mutation has a selectionCoeff of s, the multiplicative fitness effect of the mutation in a homozygote is 1+s; in a heterozygote it is 1+hs, where h is the dominance coefficient kept by the mutation type (see section 25.11.1). Note that this property has a quirk: it is stored internally in SLiM using a single-precision float, not the double-precision float type normally used by Eidos. This means that if you set a mutation mut's selection coefficient to some number x, mut.selectionCoeff==x may be F due to floating-point rounding error. Comparisons of floating-point numbers for exact equality is often a bad idea, but this is one case where it may fail unexpectedly. Instead, it is recommended to use the id or tag properties to identify particular mutations.
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: The identifier of the subpopulation in which this mutation arose. This property can be used to track the ancestry of mutations through their subpopulation of origin. For an overview of other ways of tracking genetic ancestry, including true local ancestry at each position on the chromosome, see sections 1.7 and 14.7. If you don't care which subpopulation a mutation originated in, the subpopID may be used as an arbitrary integer "tag" value for any purpose you wish; SLiM does not do anything with the value of subpopID except propagate it to Substitution objects and report it in output. (It must still be >= 0, however, since SLiM object identifiers are limited to nonnegative integers).
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined integer value. The value of tag is initially undefined, and it is an error to try to read it; if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code. The value of tag is not used by SLiM; it is free for you to use.
Other Mutation:
setMutationType(),
setSelectionCoeff()