Compute proportion of shared alleles
The function propShared computes the proportion of
shared alleles in a set of genotypes (i.e. from a genind
object). Current implementation works for any level of ploidy.
propShared(obj)
obj |
a genind object. |
Computations of the numbers of shared alleles are done in C. Proportions are computed from all available data, i.e. proportion can be computed as far as there is at least one typed locus in common between two genotypes.
Returns a matrix of proportions
Thibaut Jombart t.jombart@imperial.ac.uk
## Not run: ## make a small object data(microbov) obj <- microbov[1:5, loc = locNames(microbov)[1:2]] ## verify results propShared(obj) genind2df(obj,sep="|") ## Use this similarity measure inside a PCoA ## ! This is for illustration only ! ## the distance should be rendered Euclidean before ## (e.g. using cailliez from package ade4). matSimil <- propShared(microbov) matDist <- exp(-matSimil) D <- cailliez(as.dist(matDist)) pcoa1 <- dudi.pco(D,scannf=FALSE,nf=3) s.class(pcoa1$li,microbov$pop,lab=popNames(microbov)) ## End(Not run)
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