R: Allelic Sharing Distance

dist.asd {pegas} | R Documentation

## Allelic Sharing Distance

### Description

This function computes the allelic sharing distance (ASD) for diploid genotypes.

### Usage

    dist.asd(x, scaled = TRUE)
    dist.snp(x, scaled = TRUE)

### Arguments

`x` | an object of class `"loci"`.
`scaled` | a logical value specifying whether the distances should be scaled by the number of loci.

### Details

The ASD between two diploid genotypes is (Gao and Martin, 2009):

(1/L)sum d_j, j = 1, ... L

where L is the number loci, d_j is the value for the jth locus: 0 if both genotypes are identical, 1 if they have one allele in common, or 2 if they have no allele in common.

`dist.asd` works for all diploid genotypes (phased or unphased, with two alleles or more). Note that the required conditions are not checked by the present function: see the functions below.

### Value

an object of class `"dist"`.

### Note

`dist.snp` will be removed soon; it currently calls `dist.asd` with a warning.

### Author(s)

Emmanuel Paradis

### References

Gao, X. and Martin, E. R. (2009) Using allele sharing distance for detecting human population stratification. Human Hederity, 68, 182–191.

### See Also

`is.snp`, `is.phased`, `getPloidy`

### Examples

    data(jaguar)
    ## ASD for micro-satellites:
    d <- dist.asd(jaguar)
    co <- rainbow(nlevels(jaguar$pop))
    plot(nj(d), "u", tip.color = co[jaguar$pop], font = 2, lab4 = "a")
    legend("topleft", legend = levels(jaguar$pop), text.col = co, text.font = 2)

[Package pegas version 0.13 Index]