pegas (version 0.11)

dist.snp: Allelic Sharing Distance with SNPs

Description

These two functions compute the allelic sharing distance (ASD). dist.snp works with (strict) SNPs and is much faster than dist.asd (see below).

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.snp works only with biallelic, unphased, diploid genotypes. (These do not actually need to be SNPs: for instance, they could be A/A, A/a, and a/a). Note that the required conditions are not checked by the present function: see the functions below.

dist.asd works for all diploid genotypes (phased or unphased, with two alleles or more).

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)
# }