Defines a stutter type to be used in the allele specific stutter model.

Usage

stutter_type(
  name,
  delta,
  applies_to_all_loci = TRUE,
  stutter_regression,
  stutter_exceptions,
  applies_to_loci,
  repeat_length_by_marker
)

Arguments

name: Character. Name of the stutter, e.g. "BackStutter"
delta: Numeric. When length one, repeat units gained (lost when negative). When length two, the second element is the number of base pairs gained (lost).
applies_to_all_loci: Logical. Defaults to TRUE.
stutter_regression: Function. See read_stutter_regression.
stutter_exceptions: Optionally a list. See read_stutter_exceptions.
applies_to_loci: Optionally a character vector of locus names to which this stutter type applies.
repeat_length_by_marker: Optionally a named integer vector with repeat lengths by marker. Only needed when delta is of length two.

Value

Object of class stutter_type to be passed to allele_specific_stutter_model.

Details

When a pg_model is constructed (see log_normal_model), a stutter model can optionally be applied.

Examples

filename_bs_exceptions <- system.file("extdata",
"GlobalFiler_Stutter_Exceptions_3500.csv",package = "simDNAmixtures")
bs_exceptions <- read_stutter_exceptions(filename_bs_exceptions)

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

backstutter <- stutter_type(name = "BackStutter", delta = -1,
                            stutter_regression = bs_regression,
                            stutter_exceptions = bs_exceptions)