sample_mixture_from_genotypes {simDNAmixtures}

Sample mixture profile with provided genotypes

Description

Sample mixture profile with provided genotypes

Usage

sample_mixture_from_genotypes(genotypes, model, sample_name = "mixture")

Arguments

genotypes

List of contributor genotypes. See sample_contributor_genotypes.

model

pg_model object.

sample_name

Character. Defaults to "mixture".

Details

A mixture profile is sampled according to the provided pg_model (see gamma_model, log_normal_model and genotypes (see sample_contributor_genotypes).

Value

DataFrame with at least SMASH columns (see SMASH_to_wide_table). Depending on the chosen pg_model (e.g. gamma_model or log_normal_model), other columns with further details about the simulation are returned as well.

See Also

sample_mixtures for a function that samples many mixtures in one go.

Examples

# read allele frequencies and kit data
freqs <- read_allele_freqs(system.file("extdata","FBI_extended_Cauc.csv",
                           package = "simDNAmixtures"))
data(gf)

# define a pedigree of siblings S1 and S2 (and their parents)
ped_sibs <- pedtools::nuclearPed(children = c("S1", "S2"))

# sample genotypes for a mixture of S1 + U1 + S2
# where U1 is an unrelated person
genotypes <- sample_contributor_genotypes(contributors = c("S1","U1","S2"),
freqs, ped_sibs, loci = gf$autosomal_markers)

# define a gamma model for peak heights
gamma_model <- gamma_model(mixture_proportions = c(0.5, 0.3, 0.2), mu = 1000.,
                    cv = 0.1, model_settings = gf$gamma_settings_no_stutter)

# sample mixture from genotypes
mix <- sample_mixture_from_genotypes(genotypes, gamma_model)