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

prepareC

R Documentation

prepareC

Description

Used for preparing C++ calls

Usage

prepareC(
  nC,
  samples,
  popFreq,
  refData,
  condOrder,
  knownRef,
  kit,
  BWS,
  FWS,
  AT,
  pC,
  lambda,
  fst,
  knownRel,
  ibd,
  minF,
  normalize,
  adjFragQallele
)

Arguments

`nC`	Number of contributors in model.
`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 has locus-list element [[i]] with a list element 'r' which contains a 2 long vector with alleles for each references.
`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.
`kit`	shortname of kit: Obtained from getKit()
`BWS`	Boolean of whether back-stutter model should be used
`FWS`	Boolean of whether for-stutter model should be used
`AT`	The analytical threshold given. Used when considering probability of allele drop-outs.
`pC`	A numeric for allele drop-in probability. Default is 0.
`lambda`	Parameter in modeled peak height shifted exponential model. Default is 0.
`fst`	is the coancestry coeffecient. Default is 0.
`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)
`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.
`adjFragQallele`	Indicate whether fragmenth length of Q-allele is based on averaged weighted with frequencies