Sample genotypes for mixture contributors according to allele frequencies
sample_contributor_genotypes.RdSample genotypes for mixture contributors according to allele frequencies
Usage
sample_contributor_genotypes(
contributors,
freqs,
linkage_map,
pedigree,
loci = names(freqs),
return_non_contributors = FALSE,
sex_locus_name = "AMEL"
)Arguments
- contributors
Character vector with unique names of contributors. Valid names are "U1", "U2", ... for unrelated contributors or the names of pedigree members for related contributors.
- freqs
Allele frequencies (see read_allele_freqs)
- linkage_map
(optional) A linkage map specifying the recombination fractions between loci. If missing, loci are assumed to be independent. See also sample_many_pedigree_genotypes.
- pedigree
(optional) ped object
- loci
Character vector of locus names (defaults to
namesattribute offreqs)- return_non_contributors
Logical. Should genotypes of non-contributing pedigree members also be returned?
- sex_locus_name
Character vector, defaults to "AMEL"
Value
List of DataFrames with genotypes for each pedigree member. See sample_genotype for the DataFrame format.
Details
For each founder or unrelated person, a genotype is sampled randomly by drawing two alleles from allele frequencies. The non-founders get genotypes by allele dropping, see sample_pedigree_genotypes for details.
Examples
# read allele frequencies
freqs <- read_allele_freqs(system.file("extdata","FBI_extended_Cauc_022024.csv",
package = "simDNAmixtures"))
# 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
sample_contributor_genotypes(contributors = c("S1","U1","S2"),
freqs, pedigree = ped_sibs,
loci = gf_configuration()$autosomal_markers)
#> $S1
#> Sample Name Locus Allele1 Allele2
#> 1 S1 D3S1358 16 16
#> 2 S1 vWA 17 18
#> 3 S1 D16S539 11 11
#> 4 S1 CSF1PO 11 12
#> 5 S1 TPOX 8 8
#> 6 S1 D8S1179 11 13
#> 7 S1 D21S11 29 29
#> 8 S1 D18S51 14 18
#> 9 S1 D2S441 11 11.3
#> 10 S1 D19S433 14 14
#> 11 S1 TH01 7 9.3
#> 12 S1 FGA 22 22
#> 13 S1 D22S1045 11 15
#> 14 S1 D5S818 11 11
#> 15 S1 D13S317 10 12
#> 16 S1 D7S820 9 12
#> 17 S1 SE33 28.2 29.2
#> 18 S1 D10S1248 13 16
#> 19 S1 D1S1656 15 15
#> 20 S1 D12S391 19 22
#> 21 S1 D2S1338 17 20
#>
#> $U1
#> Sample Name Locus Allele1 Allele2
#> 1 U1 D3S1358 17 17
#> 2 U1 vWA 18 19
#> 3 U1 D16S539 11 12
#> 4 U1 CSF1PO 12 13
#> 5 U1 TPOX 8 8
#> 6 U1 D8S1179 12 13
#> 7 U1 D21S11 30 30
#> 8 U1 D18S51 12 12
#> 9 U1 D2S441 11 15
#> 10 U1 D19S433 14 15.2
#> 11 U1 TH01 6 6
#> 12 U1 FGA 22 25
#> 13 U1 D22S1045 14 16
#> 14 U1 D5S818 11 11
#> 15 U1 D13S317 12 14
#> 16 U1 D7S820 10 10
#> 17 U1 SE33 16 17
#> 18 U1 D10S1248 13 13
#> 19 U1 D1S1656 12 15
#> 20 U1 D12S391 19.3 22
#> 21 U1 D2S1338 25 25
#>
#> $S2
#> Sample Name Locus Allele1 Allele2
#> 1 S2 D3S1358 14 16
#> 2 S2 vWA 16 17
#> 3 S2 D16S539 11 12
#> 4 S2 CSF1PO 10 12
#> 5 S2 TPOX 8 8
#> 6 S2 D8S1179 15 16
#> 7 S2 D21S11 29 32.2
#> 8 S2 D18S51 13 18
#> 9 S2 D2S441 11 11
#> 10 S2 D19S433 13 14
#> 11 S2 TH01 7 9.3
#> 12 S2 FGA 22 23
#> 13 S2 D22S1045 11 16
#> 14 S2 D5S818 10 12
#> 15 S2 D13S317 12 13
#> 16 S2 D7S820 9 11
#> 17 S2 SE33 17 19
#> 18 S2 D10S1248 13 16
#> 19 S2 D1S1656 11 15
#> 20 S2 D12S391 22 22
#> 21 S2 D2S1338 19 24
#>
# now also include AMEL
sample_contributor_genotypes(contributors = c("S1","S2", "U1"),
freqs, pedigree = ped_sibs,
loci = c(gf_configuration()$autosomal_markers, "AMEL"))
#> $S1
#> Sample Name Locus Allele1 Allele2
#> 1 S1 D3S1358 18 18
#> 2 S1 vWA 15 17
#> 3 S1 D16S539 11 14
#> 4 S1 CSF1PO 10 12
#> 5 S1 TPOX 8 8
#> 6 S1 D8S1179 13 13
#> 7 S1 D21S11 30 31
#> 8 S1 D18S51 12 17
#> 9 S1 D2S441 11 14
#> 10 S1 D19S433 13 13
#> 11 S1 TH01 8 8
#> 12 S1 FGA 22 25
#> 13 S1 D22S1045 16 16
#> 14 S1 D5S818 11 13
#> 15 S1 D13S317 11 11
#> 16 S1 D7S820 10 11
#> 17 S1 SE33 19 19
#> 18 S1 D10S1248 15 16
#> 19 S1 D1S1656 12 15
#> 20 S1 D12S391 17 19
#> 21 S1 D2S1338 17 18
#> 22 S1 AMEL X Y
#>
#> $S2
#> Sample Name Locus Allele1 Allele2
#> 1 S2 D3S1358 14 18
#> 2 S2 vWA 15 17
#> 3 S2 D16S539 12 14
#> 4 S2 CSF1PO 11 12
#> 5 S2 TPOX 8 8
#> 6 S2 D8S1179 13 13
#> 7 S2 D21S11 28 30
#> 8 S2 D18S51 10 14
#> 9 S2 D2S441 10 11
#> 10 S2 D19S433 13 14
#> 11 S2 TH01 8 9
#> 12 S2 FGA 22 23
#> 13 S2 D22S1045 15 16
#> 14 S2 D5S818 11 13
#> 15 S2 D13S317 8 11
#> 16 S2 D7S820 10 11
#> 17 S2 SE33 12 18
#> 18 S2 D10S1248 13 15
#> 19 S2 D1S1656 12 15
#> 20 S2 D12S391 17 19
#> 21 S2 D2S1338 17 18
#> 22 S2 AMEL X Y
#>
#> $U1
#> Sample Name Locus Allele1 Allele2
#> 1 U1 D3S1358 16 17
#> 2 U1 vWA 15 19
#> 3 U1 D16S539 11 12
#> 4 U1 CSF1PO 12 12
#> 5 U1 TPOX 8 9
#> 6 U1 D8S1179 14 14
#> 7 U1 D21S11 29 31
#> 8 U1 D18S51 16 17
#> 9 U1 D2S441 11 11
#> 10 U1 D19S433 13 15.2
#> 11 U1 TH01 8 9.3
#> 12 U1 FGA 21 21
#> 13 U1 D22S1045 15 17
#> 14 U1 D5S818 13 13
#> 15 U1 D13S317 12 13
#> 16 U1 D7S820 11 12
#> 17 U1 SE33 25.2 27.2
#> 18 U1 D10S1248 13 14
#> 19 U1 D1S1656 15 18.3
#> 20 U1 D12S391 18 19
#> 21 U1 D2S1338 20 22
#> 22 U1 AMEL X X
#>