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.