allPairsLR {relSim}

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)

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.

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).

Author(s)

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