dbExpect | R Documentation |
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.
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 )
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 |
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 |
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? |
Computes the expected cell counts using a recursion formula. See Tvedebrink et al (2011) for details.
Returns a matrix (or vector, see above) of expected cell counts.
James Curran and Torben Tvedebrink
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.
## 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)
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