rflexdog: Simulate GBS data from the 'flexdog' likelihood.

In dcgerard/updog: Flexible Genotyping for Polyploids

Simulate GBS data from the flexdog likelihood.

Description

This will take a vector of genotypes and a vector of total read-counts, then generate a vector of reference counts. To get the genotypes, you could use rgeno. The likelihood used to generate read-counts is described in detail in Gerard et. al. (2018).

Usage

rflexdog(sizevec, geno, ploidy, seq = 0.005, bias = 1, od = 0.001)

Arguments

sizevec	A vector of total read-counts for the individuals.
geno	A vector of genotypes for the individuals. I.e. the number of reference alleles each individual has.
ploidy	The ploidy of the species.
seq	The sequencing error rate.
bias	The bias parameter. Pr(a read after selected) / Pr(A read after selected).
od	The overdispersion parameter. See the Details of the rho variable in betabinom.

Value

A vector the same length as sizevec. The ith element is the number of reference counts for individual i.

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301468")}.

• Gerard, David, and Luís Felipe Ventorim Ferrão. "Priors for genotyping polyploids." Bioinformatics 36, no. 6 (2020): 1795-1800. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btz852")}.

See Also

rgeno for a way to generate genotypes of individuals. rbetabinom for how we generate the read-counts.

Examples

set.seed(1)
n       <- 100
ploidy  <- 6

## Generate the genotypes of individuals from an F1 population,
## where the first parent has 1 copy of the reference allele
## and the second parent has two copies of the reference
## allele.
genovec <- rgeno(n = n, ploidy = ploidy, model = "f1",
                 p1geno = 1, p2geno = 2)

## Get the total number of read-counts for each individual.
## Ideally, you would take this from real data as the total
## read-counts are definitely not Poisson.
sizevec <- stats::rpois(n = n, lambda = 200)

## Generate the counts of reads with the reference allele
## when there is a strong bias for the reference allele
## and there is no overdispersion.
refvec  <- rflexdog(sizevec = sizevec, geno = genovec,
                    ploidy = ploidy, seq = 0.001,
                    bias = 0.5, od = 0)

## Plot the simulated data using plot_geno.
plot_geno(refvec = refvec, sizevec = sizevec,
          ploidy = ploidy, seq = 0.001, bias = 0.5)

dcgerard/updog documentation built on Jan. 4, 2024, 1:08 p.m.