dbExpect: Expected value of cell counts in DNA database comparison

In DNAtools: Tools for Analysing Forensic Genetic DNA Data

Expected value of cell counts in DNA database comparison

Description

Computes the expected number of cell counts when comparing DNA profiles in a DNA database. For every pair of DNA profiles in a database the number of matching and partial matching loci is recorded. A match is declared if the two DNA profiles coincide for both alleles in a locus and a partial-match is recorded if only one allele is shared between the profiles. With a total of L loci the number of matching loci is 0,...,L and partial number of matches is 0,...,L-m, where m is the number of matching loci.

Usage

dbExpect(
  probs,
  theta = 0,
  k = c(0, 0, 1),
  n = 1,
  r = 0,
  R = 0,
  round = FALSE,
  na = TRUE,
  vector = FALSE,
  collapse = FALSE,
  wildcard = FALSE,
  no.wildcard = NULL,
  rare.allele = FALSE,
  no.rare.allele = NULL
)

Arguments

probs	List of vectors with allele probabilities for each locus
theta	The coancestery coefficient
k	The vector of identical-by-descent probabilities, k=(k2,k1,k0), where for full-siblings k=c(1,2,1)/4. The default is k=c(0,0,1) refering to unrelated individuals.
n	Number of DNA profiles in the database
r	The probability assigned to the rare alleles (see rare allele matching). If a vector must be of same length as probs.
R	The probability assigned to alleles shorter or longer than allelic ladder (see rare allele matching). If a vector must be of length 1 or 2, and if a list it must be same length as probs.
round	Whether or not the results should be rounded or not
na	Whether or not the off-elements should be returned as 0 or NA
vector	Whether or not the result should be returned as a matrix or vector. Note if 'collapse' is TRUE vector is ignored.
collapse	Logical (default FALSE). If TRUE the (m,p)-matrix will be collapased into a (2*m+p)-vector containing the total number of matching alleles.
wildcard	Should wildcards be used?
no.wildcard	Should 'w' wildcards be used?
rare.allele	Should rare allele matching be used?
no.rare.allele	Should 'r' rare allele loci be used?

Details

Computes the expected cell counts using a recursion formula. See Tvedebrink et al (2011) for details.

Value

Returns a matrix (or vector, see above) of expected cell counts.

Author(s)

James Curran and Torben Tvedebrink

References

T Tvedebrink, PS Eriksen, J Curran, HS Mogensen, N Morling. 'Analysis of matches and partial-matches in Danish DNA reference profile database'. Forensic Science International: Genetics, 2011.

Examples

  ## Not run: 
  ## Simulate some allele frequencies:
  freqs <-  replicate(10, { g = rgamma(n=10,scale=4,shape=3); g/sum(g)},
              simplify=FALSE)
  ## Compute the expected number for a DB with 10000 profiles:
  dbExpect(freqs,theta=0,n=10000)
  
## End(Not run) 

DNAtools documentation built on March 18, 2022, 7:01 p.m.