This function computes likelihood ratios (LRs) for a list of pedigrees. One of the pedigrees (the last one, by default) is designated as 'reference', to be used in the denominator in all LR calculations. To ensure that all pedigrees use the same data set, one of the pedigrees may be chosen as 'source', from which data is transferred to all the other pedigrees.
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Pedigree alternatives. Each argument should be either a single
It is also possible to pass a single
An index or name indicating which of the input pedigrees should be used as "reference pedigree", i.e., used in the denominator of each LR. If NULL (the default), the last pedigree is used as reference.
An index or name designating one of the input pedigrees as
source for marker data. If given, marker data is transferred from this to
all the other pedigrees (replacing any existing markers). The default
A vector of marker names or indices indicating which markers should be included. If NULL (the default) all markers are used.
Either NULL (default), or a data frame with three columns: chromosome; marker name; centiMorgan position. If given, it signifies to the program that the markers are linked and invokes MERLIN for computing the likelihoods.
By default, all markers are assumed to be unlinked. To accommodate linkage, a
genetic map should be supplied with the argument
linkageMap. This requires
the software MERLIN to be installed.
LRresult object, which is essentially a list with entries
LRtotal : A vector of length
L is the number of input
pedigrees. The i'th entry is the total LR (i.e., the product over all
markers) comparing pedigree
i to the reference pedigree. The entry
corresponding to the reference will always be 1.
LRperMarker : A numerical matrix, where the i'th column contains the
marker-wise LR values comparing pedigree
i to the reference. The product
of all entries in a column should equal the corresponding entry in
likelihoodsPerMarker : A numerical matrix of the same dimensions as
LRperMarker, but where the entries are likelihood of each pedigree for
time : Elapsed time
Magnus Dehli Vigeland and Thore Egeland
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# Simulate 5 markers for a pair of full sibs ids = c("A", "B") sibs = nuclearPed(children = ids) sibs = simpleSim(sibs, N = 5, alleles = 1:4, ids = ids, seed = 123) # Create two alternative hypotheses halfsibs = relabel(halfSibPed(), old = 4:5, new = ids) unrel = list(singleton("A"), singleton("B")) # Compute LRs. By default, the last ped is used as reference kinshipLR(sibs, halfsibs, unrel) # Input pedigrees can be named, reflected in the output kinshipLR(S = sibs, H = halfsibs, U = unrel) # Select non-default reference (by index or name) kinshipLR(S = sibs, H = halfsibs, U = unrel, ref = "H") # Alternative syntax: List input peds = list(S = sibs, H = halfsibs, U = unrel) kinshipLR(peds, ref = "H", source = "S", verbose = TRUE) # Detailed results res = kinshipLR(peds) res$LRperMarker res$likelihoodsPerMarker
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