calculateStutter: 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.

Value

data.frame with extracted result.

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! Labelled 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.