calcQualMLE: calcQualMLE

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

calcQualMLE

Description

Optimizing the likelihood function based on qualitative model (LRmix).

Usage

calcQualMLE(
  nC,
  samples,
  popFreq,
  refData = NULL,
  condOrder = NULL,
  knownRef = NULL,
  prC = 0.05,
  fst = 0,
  prDcontr = NULL,
  prDcommon = NULL,
  steptol = 1e-06,
  prDv0 = c(0.1, 0.35, 0.7),
  maxIter = 10000
)

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.
prC	A numeric for allele drop-in probability. Can be a vector (must contain the marker names). Default is 0.
fst	The co-ancestry coefficient. Can be a vector (must contain the marker names). Default is 0.
prDcontr	assumed known dropout parameter for all contributors, NA means to be optimized. Must be a nC long vector if given.
prDcommon	vector indicating which contributors should share common drop-out parameter. Assign integers to contributors with common parameters. NA means not optimized.
steptol	Argument used in the nlm function for faster return from the optimization (tradeoff is lower accuracy).
prDv0	Start values for fitting the drop-out probabilities (will be spanned if multidimensional)
maxIter	Maximum number of iterations for nlm

Value

ret A list(fit,model,nDone,delta,seed,prepareC) where fit is Maximixed likelihood elements for given model.

Author(s)

Oyvind Bleka

Examples

## Not run: 
AT = 50 #analytical threshold
sep0 = .Platform$file.sep
popfn = paste(path.package("euroformix"),"FreqDatabases",paste0(kit,"_Norway.csv"),sep=sep0)
evidfn = paste(path.package("euroformix"),"examples",paste0(kit,"_3p.csv"),sep=sep0)
reffn = paste(path.package("euroformix"),"examples",paste0(kit,"_refs.csv"),sep=sep0)
popFreq = freqImport(popfn)[[1]] #population frequencies
samples = sample_tableToList(tableReader(evidfn)) #evidence samples
refData = sample_tableToList(tableReader(reffn)) #reference sample
dat = prepareData(samples,refData,popFreq,threshT=AT) #needed for qual method
condOrder = c(1,2,0) #assuming C1=ref1,C2=ref2
logLik1 = calcQualMLE(2,dat$samples,dat$popFreq,dat$refData,condOrder)$loglik
logLik2 = calcQualMLE(3,dat$samples,dat$popFreq,dat$refData,condOrder, prDcommon=c(1,1,2))$loglik

## End(Not run)

oyvble/euroformix documentation built on Aug. 25, 2023, 11:14 a.m.