propShared {adegenet} | R Documentation |
The function propShared
computes the proportion of
shared alleles in a set of genotypes (i.e. from a genind
object).
propShared(obj)
obj |
a genind object. |
Computations of the proportion of shared alleles are computed 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 jombart@biomserv.univ-lyon1.fr
## make a small object data(microbov) obj <- microbov[1:5,microbov@loc.fac %in% c("L01","L02")] ## 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 quasieuclid from package ade4). if(require(ade4)){ matSimil <- propShared(microbov) matDist <- exp(-matSimil) D <- as.dist(matDist) pcoa1 <- dudi.pco(D,scannf=FALSE,nf=3) s.class(pcoa1$li,microbov$pop,lab=microbov$pop.names) }