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.
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 firstname.lastname@example.org
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
## 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.