Simulating YSTR profiles

In addition to autosomal profiles, it is also possible to sample YSTR profiles.

Example

We start by reading the YSTR kit and stutter data.

  require(simDNAmixtures)
#> Loading required package: 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)

Sample Name	Locus	Allele1	Allele2
K1	DYS576	18	NA
K1	DYS389I	13	NA
K1	DYS635	23	NA
K1	DYS389II	29	NA
K1	DYS627	22	NA
K1	DYS460	11	NA
K1	DYS458	17	NA
K1	DYS19	14	NA
K1	YGATAH4	11	NA
K1	DYS448	19	NA
K1	DYS391	11	NA
K1	DYS456	16	NA
K1	DYS390	24	NA
K1	DYS438	12	NA
K1	DYS392	13	NA
K1	DYS518	41	NA
K1	DYS570	18	NA
K1	DYS437	15	NA
K1	DYS385	12	13
K1	DYS449	29	NA
K1	DYS393	13	NA
K1	DYS439	11	NA
K1	DYS481	22	NA
K1	DYF387S1	34	36
K1	DYS533	12	NA

Sample Name	Locus	Allele1	Allele2
K2	DYS576	17	NA
K2	DYS389I	13	NA
K2	DYS635	23	NA
K2	DYS389II	29	NA
K2	DYS627	21	NA
K2	DYS460	10	NA
K2	DYS458	17	NA
K2	DYS19	14	NA
K2	YGATAH4	12	NA
K2	DYS448	19	NA
K2	DYS391	11	NA
K2	DYS456	15	NA
K2	DYS390	23	NA
K2	DYS438	12	NA
K2	DYS392	13	NA
K2	DYS518	40	NA
K2	DYS570	18	NA
K2	DYS437	15	NA
K2	DYS385	11	14
K2	DYS449	28	NA
K2	DYS393	13	NA
K2	DYS439	12	NA
K2	DYS481	22	NA
K2	DYF387S1	35	36
K2	DYS533	11	NA

Simulation

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
# add results_directory="..." to save results to disk

Maarten Kruijver

2024-12-18

Example

Simulation