propShared: Compute proportion of shared alleles

In thibautjombart/adegenet: Exploratory Analysis of Genetic and Genomic Data

Compute proportion of shared alleles

Description

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.

Usage

propShared(obj)

Arguments

obj	a genind object.

Details

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.

Value

Returns a matrix of proportions

Author(s)

Thibaut Jombart [e-mail]

See Also

dist.genpop

Examples

## 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)

thibautjombart/adegenet documentation built on Feb. 9, 2023, 5:50 p.m.