R: Compute proportion of shared alleles

propShared {adegenet} | R Documentation

## 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 t.jombart@imperial.ac.uk

### 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)

[Package adegenet version 2.1.4 Index]