relSim (version 1.0.0)

allPairsLR: Compute the likehood ratio for all pairs of profiles in a database

Description

This function takes every pair of profiles in a database of profiles and computes the likelihood ratio (LR) for a specific relationship given by nCode. That means there will be \(N(N-1)/2\) LRs computed for N profiles.

Usage

allPairsLR(Profiles, listFreqs, nCode)

Value

a NumericVector containing the LRs. They are stored in sequential order so if for example there were three profiles, then there are 3 possible LRs, and the result vector would contain the LRs for the profile pairs (1, 2), (1, 3), and (2, 3).

Arguments

Profiles

an integer vector of stacked profiles representing the database. This vector has \(2NL\) entries, where N is the number of profiles and \(L\) is the number of loci.

listFreqs

is a set of allele frequencies representing a particular multiplex. The function assumes that that loci in the profiles are in the same order as the loci in this list. The data structure is a List of NumericVector's.

nCode

if 1 then compute the LR for siblings, otherwise computer the LR for parent/child.

Author

James Curran

Examples

data("USCaucs")
N = 600
profs = relSim:::.randomProfiles(USCaucs$freqs, N)
system.time({lr = relSim:::allPairsLR(profs, USCaucs$freqs, 1)})
plot(density(log10(lr)))
mean(lr > 1) ## estimate the probability that the LR is incorrectly above 1