LRstat: Distribution of LR(HP) and LR(HD)

Description

Distribution of LR(HP) and LR(HD) are calculated as well as some summary statistics.

Usage

LRstat(ped_claim, ped_true, ids, alleles, afreq = NULL, 
known_genotypes = list(), loop_breakers = NULL, Xchrom = F, plot = T)

Arguments

ped_claim

a linkdat object, or a list of several linkdat and/or singleton objects, describing the claimed relationship. If a list, the sets of ID labels must be disjoint, that is, all ID labels must be unique.

ped_true

a linkdat object, or a list of several linkdat and/or singleton objects, describing the true relationship. ID labels must be consistent with ped_claim. individuals available for genotyping.

ids

individuals available for genotyping.

alleles

a numeric or character vector containing marker alleles names

afreq

a numerical vector with allele frequencies. An error is given if they don't sum to 1 (rounded to 3 decimals).

known_genotypes

list of triplets (a, b, c), indicating that individual a has genotype b/c.

loop_breakers

a numeric containing IDs of individuals to be used as loop breakers. Relevant only if any of the pedigrees has loops. See breakLoops.

Xchrom

a logical: Is the marker on the X chromosome?

plot

either a logical or the character "plot_only", controlling if a plot should be produced. If "plot_only", a plot is drawn, but no further computations are done (useful for reproducing the plot in computer-intensive applications)

Value

main: Expected values, variances of LR(HP) and LR(HD). RMNE
extra: P(data|ped_claim) and P(data|ped_true)
LRdist: Distribution of LR

Details

Connected to joint work with Klaas Slooten

Examples

Run this code

HP = nuclearPed(noffs=1, sex=2) # Specifies individual 1 as the father of 3
HD= list(singleton(id=1,sex=1), singleton(id=3, sex=2)) # Specifies 1 and 3 as unrelated
p=c(0.2,0.3,0.5);L=length(p)
available = c(1, 3)
res=LRstat(HP, HD, available, alleles = 1:L, afreq=p)
E.LR.HP=res$main[1]
stopifnot(abs(E.LR.HP-(L+3)/4)<1e-06)
res$LRdist #Distribution of LR