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

contLikMLE

R Documentation

contLikMLE

Description

contLikMLE optimizes the likelihood function of the DNA mixture model

Usage

contLikMLE(
  nC,
  samples,
  popFreq,
  refData = NULL,
  condOrder = NULL,
  knownRef = NULL,
  xi = 0,
  prC = 0,
  nDone = 2,
  threshT = 50,
  fst = 0,
  lambda = 0,
  pXi = function(x) 1,
  delta = 1,
  kit = NULL,
  verbose = TRUE,
  difftol = 0.01,
  knownRel = NULL,
  ibd = c(1, 0, 0),
  xiFW = 0,
  pXiFW = function(x) 1,
  seed = NULL,
  maxThreads = 0,
  steptol = 0.001
)

Arguments

`nC`	Number of contributors in model. Must be a constant.
`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 (2-size) allele-vector given in list element [[i]][[s]].
`condOrder`	Specify conditioning references from refData (must be consistent order). For instance condOrder=(0,2,1,0) means that we restrict the model such that Ref2 and Ref3 are respectively conditioned as 2. contributor and 1. contributor in the model.
`knownRef`	Specify known non-contributing references from refData (index). For instance knownRef=(1,2) means that reference 1 and 2 is known non-contributor in the hypothesis. This affectes coancestry correction.
`xi`	A numeric giving stutter-ratio if it is known. Default is 0, meaning stutter is not used.
`prC`	A numeric for allele drop-in probability. Can be a vector (must contain the marker names). Default is 0.
`nDone`	Number of optimizations required providing equivalent results (same logLik value obtained)
`threshT`	The detection threshold given. Used when considering probability of allele drop-outs. Can be a vector (must contain the marker names).
`fst`	The co-ancestry coefficient. Can be a vector (must contain the marker names). Default is 0.
`lambda`	Parameter in modeled peak height shifted exponential model. Can be a vector (must contain the marker names). Default is 0.
`pXi`	Prior function for xi-parameter (stutter). Flat prior on [0,1] is default.
`delta`	Scaling of variation of normal distribution when drawing random startpoints. Default is 1.
`kit`	Used to model degradation. Must be one of the shortnames of kit: check getKit()
`verbose`	Whether printing optimization progress. Default is TRUE.
`difftol`	Tolerance for being exact in log-likelihood value (relevant when nDone>1)
`knownRel`	gives the index of the reference which the 1st unknown is related to.
`ibd`	the identical by decent coefficients of the relationship (specifies the type of relationship)
`xiFW`	A numeric giving FW stutter-ratio if it is known.Default is 0, meaning stutter is not used.
`pXiFW`	Prior function for xiFW-parameter (FW stutter). Flat prior on [0,1] is default.
`seed`	The user can set seed if wanted
`maxThreads`	Maximum number of threads to be executed by the parallelization
`steptol`	Argument used in the nlm function for faster return from the optimization (tradeoff is lower accuracy).