calcQuanLRcomparison: calcQuanLRcomparison

In oyvble/casesolver: A software for comparing DNA profiles within cases

calcQuanLRcomparison

Description

Function calculating LR using EuroForMix for remaining matches (from Step 1)

Usage

calcQuanLRcomparison(
  DBmix,
  DBref,
  matchlist,
  popFreq,
  kit,
  xiBW = 0,
  xiFW = 0,
  pC = 0.05,
  lambda = 0.01,
  threshT = 50,
  nDone = 4,
  maxC = 3,
  nContr = NULL,
  normalize = FALSE,
  minFreq = NULL,
  useEFMex = FALSE
)

Arguments

DBmix	A list with evidence information [[sample]][[loc]] = list(adata,hdata)
DBref	A (nR x nL) matrix with reference information. LIST not efficient
matchlist	A matrix with overview of what references are matches each of samples (SampleName,Reference,MAC)
popFreq	A list of allele frequencies for a given population.
kit	Used to model degradation. Must be one of the shortnames of kit: Returned by euroformix::getKit()
xiBW	Model parameter for Backward stutter. NULL indicates stutter model.
xiFW	Model parameter for Forward stutter. NULL indicates stutter model.
pC	A numeric for allele drop-in probability.
lambda	Parameter in modeled peak height shifted exponential model.
threshT	The detection threshold given.
nDone	Maximum number of random evaluations nlm-optimizing routing. Default is 4.
maxC	Maximum number of contributors possible to assume. Default is 3.
nContr	A vector of number of contributors for each of the row in the matchlist. If NULL (default), the max(nA)/2 rule is applied.
normalize	A boolean of whether normalization should be applied or not.
minFreq	The freq value included for new alleles. Default NULL is using min.observed in popFreq.
useEFMex	Whether the exhaustive method should be used

oyvble/casesolver documentation built on Feb. 26, 2025, 2:05 a.m.