rgeno {updog}

Simulate individual genotypes from one of the supported flexdog models.

Description

This will simulate genotypes of a sample of individuals drawn from one of the populations supported by flexdog. See the details of flexdog for the models allowed. These genotype distributions are described in detail in Gerard and Ferrão (2020).

Usage

rgeno(
  n,
  ploidy,
  model = c("hw", "bb", "norm", "f1", "s1", "flex", "uniform"),
  allele_freq = NULL,
  od = NULL,
  p1geno = NULL,
  p2geno = NULL,
  pivec = NULL,
  mu = NULL,
  sigma = NULL
)

Arguments

n

The number of observations.

ploidy

The ploidy of the species.

model

What form should the prior take? See Details in flexdog.

allele_freq

If model = "hw", then this is the allele frequency of the population. For any other model, this should be NULL.

od

If model = "bb", then this is the overdispersion parameter of the beta-binomial distribution. See betabinom for details. For any other model, this should be NULL.

p1geno

Either the first parent's genotype if model = "f1", or the only parent's genotype if model = "s1". For any other model, this should be NULL.

p2geno

The second parent's genotype if model = "f1". For any other model, this should be NULL.

pivec

A vector of probabilities. If model = "ash", then this represents the mixing proportions of the discrete uniforms. If model = "flex", then element i is the probability of genotype i - 1. For any other model, this should be NULL.

mu

If model = "norm", this is the mean of the normal. For any other model, this should be NULL.

sigma

If model = "norm", this is the standard deviation of the normal. For any other model, this should be NULL.

Details

List of non-NULL arguments:

model = "flex":

pivec

model = "hw":

allele_freq

model = "f1":

p1geno and p2geno

model = "s1":

p1geno

model = "uniform":

no non-NULL arguments

model = "bb":

allele_freq and od

model == "norm":

mu and sigma

Value

A vector of length n with the genotypes of the sampled individuals.

Author(s)

David Gerard

References

• Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789-807. doi:10.1534/genetics.118.301468.

• Gerard, David, and Luís Felipe Ventorim Ferrão. "Priors for genotyping polyploids." Bioinformatics 36, no. 6 (2020): 1795-1800. doi:10.1093/bioinformatics/btz852.

Examples

## F1 Population where parent 1 has 1 copy of the referenc allele
## and parent 2 has 4 copies of the reference allele.
ploidy <- 6
rgeno(n = 10, ploidy = ploidy, model = "f1", p1geno = 1, p2geno = 4)

## A population in Hardy-Weinberge equilibrium with an
## allele frequency of 0.75
rgeno(n = 10, ploidy = ploidy, model = "hw", allele_freq = 0.75)