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

Documentation for Substitution class from SLiM

1	Substitution

An object of class list of length 12.

This class has the following methods (functions):

getValue
setValue

This class has the following properties:

id: 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, and that identifier is carried over to the Substitution object when the mutation fixes.
fixationGeneration: 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 generation in which this mutation fixed.
mutationType: 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.
nucleotide: 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.
nucleotideValue: 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.
originGeneration: 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 generation in which this mutation arose.
position: 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.
selectionCoeff: 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.
subpopID: 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 value is carried over from the Mutation object directly; if a "tag” value was used in the Mutation object (see section 23.8.1), that value will carry over to the corresponding Substitution object. The subpopID in Substitution is a read- write property to allow it to be used as a "tag” in the same way, if the origin subpopulation identifier is not needed.
tag: 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 carried over automatically from the original Mutation object. Apart from that, the value of tag is not used by SLiM; it is free for you to use.