allele_specific_stutter_model: Stutter model where the expected stutter rate depends on the...

In simDNAmixtures: Simulate Forensic DNA Mixtures

Stutter model where the expected stutter rate depends on the allele and locus

Description

Stutter model where the expected stutter rate depends on the allele and locus

Usage

allele_specific_stutter_model(
  stutter_types,
  size_regression,
  sex_locus_name = "AMEL"
)

Arguments

stutter_types	List. See stutter_type.
size_regression	Function, see read_size_regression.
sex_locus_name	Character vector, defaults to "AMEL".

Details

When a pg_model is constructed (see gamma_model), a stutter model can optionally be applied. The allele specific stutter model is commonly used with a log normal model. The expected stutter ratio for a parent allele at a locus is obtained from a linear regression of observed stutter ratios against allele length. For some loci or alleles the linear model may not be satisfactory. To override the expected stutter rates for specific alleles, a list of exceptions can be used. See stutter_type for more detail.

Value

Object of class stutter_model to be used by e.g. log_normal_model.

See Also

global_stutter_model for a stutter model where the expected stutter ratio does not depend on the locus or parent allele.

Examples

# we will define an allele specific stutter model for back stutter only

# prepare stutter regression
filename_bs_regression <- system.file("extdata",
"GlobalFiler_Stutter_3500.txt",package = "simDNAmixtures")
bs_regression <- read_stutter_regression(filename_bs_regression)

# prepare exceptions, i.e. where does the regression not apply?
filename_bs_exceptions <- system.file("extdata",
"GlobalFiler_Stutter_Exceptions_3500.csv",package = "simDNAmixtures")
bs_exceptions <- read_stutter_exceptions(filename_bs_exceptions)

# prepare a stutter type
backstutter <- stutter_type(name = "BackStutter", delta = -1,
                            stutter_regression = bs_regression,
                            stutter_exceptions = bs_exceptions)

# assign stutter model
size_regression <- read_size_regression(system.file("extdata",
"GlobalFiler_SizeRegression.csv",package = "simDNAmixtures"))
bs_model <- allele_specific_stutter_model(list(backstutter), size_regression)
bs_model

simDNAmixtures documentation built on April 15, 2025, 1:11 a.m.