gl.percent.freq

This is a support script, to take SNP data or SilicoDArT presence/absence
data grouped into populations in a genlight object {adegenet} and generate
a table of allele frequencies for each population and locus

Functions are provided that facilitate 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' supports also the analysis of 3rd party software package
such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version
2.0.3 we also implemented simulation functions, that allow to forward simulate
'SNP' dynamics under different population and evolutionary dynamics.
Comprehensive tutorials and support can be found at our 'github' repository:
github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find
the information by typing citation('dartR') in the console.

Bernd Gruber

dartR

Importing and Analysing 'SNP' and 'Silicodart' Data Generated by
Genome-Wide Restriction Fragment Analysis

Arthur Georges

Jose L. Mijangos

Carlo Pacioni

Diana Robledo-Ruiz

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

gl.percent.freq function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP or Tag P/A
(SilicoDArT) data [required].</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 or as specified using gl.set.verbosity].</dd></dl>

Arguments

Custodian: Arthur Georges (Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Generates percentage allele frequencies by locus and population — gl.percent.freq

<dl>

<dt>x</dt>
<dd>Name of the genlight object containing the SNP or Tag P/A
(SilicoDArT) data [required].</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 or as specified using gl.set.verbosity].</dd>

</dl>

Custodian: Arthur Georges (Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

gl.percent.freq: Generates percentage allele frequencies by locus and population

Description

Usage

Value

Arguments

Author

Examples