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 |
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 |
See Also
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]