stamppAmova: Analysis of Molecular Variance

In StAMPP: Statistical Analysis of Mixed Ploidy Populations

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

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)

Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>

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

# 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
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 

   /// adegenet 2.1.3 is loaded ////////////

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


Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4

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 

Warning message:
In if (class(y) == "dist") y <- as.matrix(y) :
  the condition has length > 1 and only the first element will be used

StAMPP documentation built on Aug. 8, 2021, 9:07 a.m.