Analysis of Molecular Variance
Calculates an AMOVA based on the genetic distance matrix from stamppNeisD() using the amova() function from the package PEGAS for exploring within and between population variation
stamppAmova(dist.mat, geno, perm = 100)
dist.mat |
the matrix of genetic distances between individuals generated from stamppNeisD() |
geno |
a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels |
perm |
the number of permutations for the tests of hypotheses |
Uses the formula distance ~ populations, to calculate an AMOVA for population differentiation and within & between population variation. This function uses the amova function from the PEGAS package.
An object of class "amova" which is a list containing a table of sum of square deviations (SSD), mean square deviations (MSD) and the number of degrees of freedom as well as the variance components
Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>
Paradis E (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419-420. <doi:10.1093/bioinformatics/btp696>
# import genotype data and convert to allele frequecies data(potato.mini, package="StAMPP") potato.freq <- stamppConvert(potato.mini, "r") # Calculate genetic distance between individuals potato.D.ind <- stamppNeisD(potato.freq, FALSE) # Calculate AMOVA stamppAmova(potato.D.ind, potato.freq, 100)
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