updog: rgeno – R documentation

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rgeno

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)

updog

Flexible Genotyping for Polyploids

v2.0.2

GPL-3

Authors

David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)

Initial release