feat_unphased: Feature: Unphased Sequences

In statgenlmu/coala: A Framework for Coalescent Simulation

Feature: Unphased Sequences

Description

This simulates unphased data by randomly mixing the sites within one individual. Each position is randomly taken from a phased chromosome..

Usage

feat_unphased(samples_per_ind, locus_group = "all")

Arguments

samples_per_ind

The number of pseudo-chromosomes that are created from the phased chromosomes for each individual.

locus_group

The loci for which this features is used. Can either be "all" (default), in which case the feature is used for simulating all loci, or a numeric vector. In the latter case, the feature is only used for the loci added in locus_ commands with the corresponding index starting from 1 in order in which the commands where added to the model. For example, if a model has locus_single(10) + locus_averaged(10, 11) + locus_single(12) and this argument is c(2, 3), than the feature is used for all but the first locus (that is locus 2 - 12).

Details

For each individual, ploidy chromosomes are simulated, and samples_per_ind pseudo-chromosomes are created of these.

Value

The feature, which can be added to a model using +.

The feature, which can be added to a model created with coal_model using +.

See Also

For creating a model: coal_model

Other features: feat_growth(), feat_ignore_singletons(), feat_migration(), feat_mutation(), feat_outgroup(), feat_pop_merge(), feat_recombination(), feat_selection(), feat_size_change()

Examples

# Simulate unphased data in a diploid population
model <- coal_model(10, 1, ploidy = 2) +
  feat_mutation(10) +
  feat_unphased(2) +
  sumstat_seg_sites()
simulate(model)

# The same as before, but return only one chromosome for
# each individual:
model <- coal_model(10, 1, ploidy = 2) +
  feat_mutation(10) +
  feat_unphased(1) +
  sumstat_seg_sites()
simulate(model)

statgenlmu/coala documentation built on March 5, 2024, 10:49 p.m.