Qassignate: Qassignate

In oyvble/euroformix: A Quantitative Model for Interpreting DNA Mixtures

Qassignate

Description

Q-designation. It also takes care of including new/rare alleles

Usage

Qassignate(
  samples,
  popFreq,
  refData = NULL,
  doQ = TRUE,
  incR = FALSE,
  incS = FALSE,
  minF = NULL,
  normalize = FALSE,
  verbose = TRUE
)

Arguments

samples	A List with samples which for each samples has locus-list elements with list elements adata and hdata. 'adata' is a qualitative (allele) data vector and 'hdata' is a quantitative (peak heights) data vector.
popFreq	A list of allele frequencies for a given population.
refData	Reference objects with list element [[s]]$adata[[i]]. The list element has reference-list with list-element 's' having a loci-list adata with list-element 'i storing qualitative data.
doQ	Whether to Q-designate or not
incR	Whether to include reference-alleles in the Q-assignation
incS	Whether to include potential BW stutters in the Q-assignation
minF	The freq value included for new alleles (new alleles as potential stutters will have 0). Default NULL is using min.observed in popFreq.
normalize	Whether normalization should be applied or not. Default is FALSE.
verbose	Whether printing out information

Details

Assigns non-shown alleles as one single allele (the Q-allele).

Value

ret A list(popFreq,refData,samples) with Q-designated alleles.

Author(s)

Oyvind Bleka

oyvble/euroformix documentation built on May 28, 2024, 7:28 p.m.