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In addition to autosomal profiles, it is also possible to sample YSTR profiles.
We start by reading the YSTR kit and stutter data.
require(simDNAmixtures)
data_dir <- system.file("extdata", package = "simDNAmixtures")
kit_filename <- file.path(data_dir, "YFiler_Plus_3500_FSSA.xml")
YSTR_kit <- read_STRmix_kit_settings(kit_filename, data_dir, include_y_loci = TRUE)Then we input two genotypes
y_refs_with_names <- as.data.frame(readxl::read_excel(path = system.file("extdata","South_Australia_YSTRs.xlsx",
package = "simDNAmixtures"),
col_types = rep("text", 27)))
x <- y_refs_with_names[1:2, -c(1, 2)]
rownames(x) <- c("K1", "K2")
genotypes <- simDNAmixtures:::.wide_YSTR_references_to_allele_tables(x)
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sampling_parameters <- list(min_template = 250., max_template = 5000.,
degradation_shape = 2.5, degradation_scale = 5e-4)
mixtures <- sample_mixtures_from_genotypes(n = 10, genotypes = genotypes, sampling_parameters = sampling_parameters,
model_settings = YSTR_kit, sample_model = sample_log_normal_model,
number_of_replicates = 3, tag = "YSTR 2P")
length(mixtures)
#> [1] 4
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