pegas (version 0.12)

dist.asd: 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.

Value

an object of class "dist".

Details

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

$$\frac{1}{L}\sum_{j=1}^L d_j$$

where \(L\) is the number loci, \(d_j\) is the value for the \(j\)th 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.

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

# NOT RUN {
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)
# }