dist.asd | R Documentation |
This function computes the allelic sharing distance (ASD) for diploid genotypes.
dist.asd(x, scaled = TRUE, pairwise.deletion = FALSE)
x |
an object of class |
scaled |
a logical value specifying whether the distances should be scaled by the number of loci. |
pairwise.deletion |
a logical value: whether to check for missing values for each pairwise comparison (see 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.
The pairwise deletion is done with respect to missing values coded as
NA
, not on the ‘null alleles’ (‘0’ or ‘.’). You
may need to use the function nullAlleles2NA
first if
your data has genotypes with null alleles that you want to treat as
missing values.
an object of class "dist"
.
Emmanuel Paradis
Gao, X. and Martin, E. R. (2009) Using allele sharing distance for detecting human population stratification. Human Hederity, 68, 182–191.
is.snp
, is.phased
, getPloidy
,
nullAlleles2NA
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.