diff_test: An exact test of population differentiation for genind objects
Description
This function uses Fisher's exact test to determine if
alleles in sub-populations are drawn randomly from a
larger population (i.e. a significance test for allelic
differentiation among sub-populations).
Usage
diff_test(x, sim = TRUE, nreps = 2000)
Arguments
x
a genind object (from package adegenet)
sim
boolean: if TRUE simulate p-value by using an
MCMC sample of those tables that have the same marginal
totals as the observed data (required for all but the
smallest datasets)
nreps
number of steps used to simulate p-value
(default 2000)
Value
named vector of p-values testing the null hypothesis
these samples where drawn from a panmictic population.
Details
Note, this test returns p-values for each locus in a
dataset _not_ estimates of effect size. Since most
populations have some degree of population
differentiation, very large samples are almost guaranteed
to return significant results. Refer to estimates of the
various differentiation statistics (D, G''ST and
Phi'ST)to ascertain how meaningful such results might be.
See Also
fisher.test from base R, which this
function wraps