Calculate statistics for stutters.
calculateStutter(
data,
ref,
back = 2,
forward = 1,
interference = 0,
replace.val = NULL,
by.val = NULL,
debug = FALSE
)data.frame with extracted result.
data frame with genotype data. Requires columns 'Sample.Name', 'Marker', 'Allele', 'Height'.
data frame with the known profiles. Requires columns 'Sample.Name', 'Marker', 'Allele'.
integer for the maximal number of backward stutters (max size difference 2 = n-2 repeats).
integer for the maximal number of forward stutters (max size difference 1 = n+1 repeats).
integer specifying accepted level of allowed overlap.
numeric vector with 'false' stutters to replace.
numeric vector with correct stutters.
logical indicating printing debug information.
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.