stamppAmova: Analysis of Molecular Variance

Description Usage Arguments Details Value Author(s) References Examples

View source: R/stamppAmova.R

Description

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.

Usage

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stamppAmova(dist.mat, geno, perm = 100)

Arguments

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.

Details

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.

Value

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

Author(s)

LW Pembleton

References

Paradis E (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419-420. <doi:10.1093/bioinformatics/btp696>

Examples

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# 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)

Example output

Loading required package: pegas
Loading required package: ape
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'pegas'

The following object is masked from 'package:ade4':

    amova

The following object is masked from 'package:ape':

    mst


	Analysis of Molecular Variance

Call: amova(formula = dist ~ pop.names, nperm = perm)

                 SSD         MSD df
pop.names 0.10701827 0.053509133  2
Error     0.01204481 0.004014937  3
Total     0.11906308 0.023812616  5

Variance components:
             sigma2 P.value
pop.names 0.0247471  0.0792
Error     0.0040149        

Phi-statistics:
pop.names.in.GLOBAL 
          0.8604084 

Variance coefficients:
a 
2 

StAMPP documentation built on Nov. 17, 2017, 5:34 a.m.