| dist.asd {pegas} | R Documentation |
This function computes the allelic sharing distance (ASD) for diploid genotypes.
dist.asd(x, scaled = TRUE) dist.snp(x, scaled = TRUE)
x |
an object of class |
scaled |
a logical value specifying whether the distances should be scaled by the number of loci. |
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.
an object of class "dist".
dist.snp will be removed soon; it currently calls
dist.asd with a warning.
Emmanuel Paradis
Gao, X. and Martin, E. R. (2009) Using allele sharing distance for detecting human population stratification. Human Hederity, 68, 182–191.
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)