sequence_module {GenomeAdmixR}

create sequence module

Description

creates a sequence module, which contains all relevant information in order to perform a simulation based on sequence data.

Usage

sequence_module(
  molecular_data = NA,
  initial_frequencies = NA,
  morgan = 1,
  recombination_rate = NA,
  markers = NA,
  mutation_rate = 0,
  substitution_matrix = matrix(1/4, 4, 4)
)

Arguments

molecular_data

Genomic data used as input, should be of type genomeadmixr_data. Either a single dataset is provided, or a list of multiple genomeadmixr_data objects.

initial_frequencies

A vector describing the initial contribution of each provided input data set to the starting hybrid swarm. By default, equal frequencies are assumed. If a vector not summing to 1 is provided, the vector is normalized.

morgan

Length of the molecular sequence in Morgan (e.g. the number of crossovers during meiosis), alternatively, the recombination rate can be used, see below.

recombination_rate

rate in cM / Mbp, used to map recombination to the markers. If the recombination_rate is not set, the value for Morgan is used, assuming that the markers included span an entire chromosome.

markers

A vector of locations of markers, these markers are tracked for every generation.

mutation_rate

the per base probability of mutation. Default is 0.

substitution_matrix

a 4x4 matrix representing the probability of mutating to another base (where [1/2/3/4] = [a/c/t/g]), conditional on the event of a mutation happening. Default is the JC69 matrix, with equal probabilities for all transitions / transversions.

Value

sequence module object, used as starting point for simulate_admixture.