gl.amova

This script performs an AMOVA based on the genetic distance matrix from
stamppNeisD() [package StAMPP] using the amova() function from the package
PEGAS for exploring within and between population variation. For detailed
information use their help pages: ?pegas::amova, ?StAMPP::stamppAmova. Be
aware due to a conflict of the amova functions from various packages I had
to 'hack' StAMPP::stamppAmova to avoid a namespace conflict.

Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
supports the installation of all packages in the 'dartRverse'.
If you want to cite 'dartR', you find the information by typing citation('dartR.base')
in the console.

Bernd Gruber

dartR.base

Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

Ching Ching Lau

gl.amova function

<dl><dt>x</dt>
<dd>Name of the genlight containing the SNP genotypes, with
population information [required].</dd>
<dt>distance</dt>
<dd>Distance matrix between individuals (if not provided NeisD
from StAMPP::stamppNeisD is calculated) [default NULL].</dd>
<dt>permutations</dt>
<dd>Number of permutations to perform for hypothesis
testing [default 100]. Please note should be set to 1000 for analysis.</dd>
<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
progress log ; 3, progress and results summary; 5, full report
[default 2, unless specified using gl.set.verbosity].</dd></dl>

Arguments

Bernd Gruber (bugs? Post to 
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Performs AMOVA using genlight data — gl.amova

<dl>

<dt>x</dt>
<dd>Name of the genlight containing the SNP genotypes, with
population information [required].</dd>


<dt>distance</dt>
<dd>Distance matrix between individuals (if not provided NeisD
from StAMPP::stamppNeisD is calculated) [default NULL].</dd>


<dt>permutations</dt>
<dd>Number of permutations to perform for hypothesis
testing [default 100]. Please note should be set to 1000 for analysis.</dd>


<dt>verbose</dt>
<dd>Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
progress log ; 3, progress and results summary; 5, full report
[default 2, unless specified using gl.set.verbosity].</dd>

</dl>

Bernd Gruber (bugs? Post to 
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

gl.amova: Performs AMOVA using genlight data

Description

Usage

Value

Arguments

Author

Examples