sample_many_pedigree_genotypes {simDNAmixtures}R Documentation

Sample (many) genotypes for pedigree members according to allele frequencies by allele dropping and possibly taking linkage into account by simulating recombination.

Description

Sample (many) genotypes for pedigree members according to allele frequencies by allele dropping and possibly taking linkage into account by simulating recombination.

Usage

sample_many_pedigree_genotypes(
  pedigree,
  freqs,
  loci = names(freqs),
  unrelated_names = character(),
  linkage_map,
  number_of_replicates = 1L,
  sex_locus_name = "AMEL",
  return_transmission_vectors = FALSE
)

Arguments

pedigree

ped object

freqs

Allele frequencies (see read_allele_freqs)

loci

Character vector of locus names (defaults to names attribute of freqs)

unrelated_names

Character vector with names of any additional unrelated persons. Defaults to length zero.

linkage_map

A linkage map specifying cM distances between loci. If missing, loci are assumed to be independent.

number_of_replicates

An integer specifying the number of replicate genotype samples to generate. Defaults to 1.

sex_locus_name

Character vector, defaults to "AMEL"

return_transmission_vectors

Should transmission vectors be returned as an attribute? These are usually not of interest, so the default is FALSE.

See Also

read_allele_freqs

Examples

# load allele frequencies
freqs <- read_allele_freqs(system.file("extdata",
                            "FBI_extended_Cauc_022024.csv",
                            package = "simDNAmixtures"))

# define a pedigree with two full siblings: S1 and S2
ped_fs <- pedtools::nuclearPed(children = c("S1", "S2"))

# define two linked loci
linkage_map <- data.frame(chromosome = c(12, 12),
                          locus = c("vWA", "D12S391"),
                          position = c(15.15, 26.63))


# sample genotypes ignoring linkage
sample_many_pedigree_genotypes(pedigree = ped_fs, freqs = freqs,
                             loci = c("vWA", "D12S391"),
                            number_of_replicates = 10)

# sample genotypes taking linkage into acconut
sample_many_pedigree_genotypes(pedigree = ped_fs, freqs = freqs,
                            loci = c("vWA", "D12S391"),
                            linkage_map = linkage_map,
                            number_of_replicates = 10)

[Package simDNAmixtures version 1.1.2 Index]