Likelihood ratios of pedigree hypotheses
This function computes likelihood ratios for a given a list of pedigrees (linkdat/singletons objects), one of which is
the 'reference', with genotype data from the same set of markers. Data exported from the 'Familias' software can be analysed
by using Familias2linkdat prior to calling this function.
LR(x, ref, markers)
x |
A list of pedigrees. Each pedigree is either a single linkdat/singleton object, or a list of such objects (the latter is neccessary if the pedigree is disconnected). |
ref |
A single integer, indicating the index of the reference pedigree. This is used in the denominator of each LR. |
markers |
A vector of integers, indexing which markers should be included. If NULL (the default) all markers are used. |
A list with entries
LR |
Likelihood ratios |
LRperMarker |
Likelihood ratios for each marker |
likelihoodsPerSystem |
Likelihoods for each marker |
time |
user, system and elapsed time |
Magnus Dehli Vigeland and Thore Egeland
# Simulate genotypes for 5 tetraallelic markers for a pair of full sibs set.seed(123) sibs = simpleSim(nuclearPed(2), N=5, alleles=1:4, available=3:4) # Create two alternative hypotheses and transfer the simulated genotypes to them halfsibs = addOffspring(nuclearPed(1),father=1,noffs=1,id=4) halfsibs = transferMarkerdata(sibs, halfsibs) unrel = list(singleton(3), singleton(4)) unrel = transferMarkerdata(sibs, unrel) # Compute LR with 'unrelated' as reference LR(list(sibs, halfsibs, unrel), ref=3) ## Not run: data(adoption) x = Familias2linkdat(adoption$pedigrees, adoption$datamatrix, adoption$loci) result = LRparamlink(x, ref=2) result33 = LRparamlink(x, ref=2, marker=c(11,33)) ## End(Not run)
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