calculateStutter: Calculate Stutter

In OskarHansson/strvalidator: Process Control and Validation of Forensic STR Kits

Calculate Stutter

Description

Calculate statistics for stutters.

Usage

calculateStutter(
  data,
  ref,
  back = 2,
  forward = 1,
  interference = 0,
  replace.val = NULL,
  by.val = NULL,
  debug = FALSE
)

Arguments

data	data frame with genotype data. Requires columns 'Sample.Name', 'Marker', 'Allele', 'Height'.
ref	data frame with the known profiles. Requires columns 'Sample.Name', 'Marker', 'Allele'.
back	integer for the maximal number of backward stutters (max size difference 2 = n-2 repeats).
forward	integer for the maximal number of forward stutters (max size difference 1 = n+1 repeats).
interference	integer specifying accepted level of allowed overlap.
replace.val	numeric vector with 'false' stutters to replace.
by.val	numeric vector with correct stutters.
debug	logical indicating printing debug information.

Details

Calculates stutter ratios based on the 'reference' data set and a defined analysis range around the true allele.

NB! Off-ladder alleles ('OL') is NOT included in the analysis. NB! Labeled pull-ups or artefacts within stutter range IS included in the analysis.

There are three levels of allowed overlap (interference). 0 = no interference (default): calculate the ratio for a stutter only if there are no overlap between the stutter or its allele with the analysis range of another allele. 1 = stutter-stutter interference: calculate the ratio for a stutter even if the stutter or its allele overlap with a stutter within the analysis range of another allele. 2 = stutter-allele interference: calculate the ratio for a stutter even if the stutter and its allele overlap with the analysis range of another allele.

Value

data.frame with extracted result.

OskarHansson/strvalidator documentation built on July 22, 2023, 12:04 p.m.