gl2genalex

The output csv file contains the snp data and other relevant lines suitable
 for genalex. This script is a wrapper for genind2genalex
 (package poppr).

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

gl2genalex function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>
<dt>outfile</dt>
<dd>File name of the output file (including extension)
[default 'genalex.csv'].</dd>
<dt>outpath</dt>
<dd>Path where to save the output file [default tempdir()].</dd>
<dt>overwrite</dt>
<dd>If FALSE and filename exists, then the file will not be
overwritten. Set this option to TRUE to overwrite the file [default FALSE].</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: Luis Mijangos, Author: Katrin Hohwieler, wrapper Arthur
Georges (Post to <a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>)

Author

Converts a genlight object into a format suitable for input to genalex — gl2genalex

<dl>

<dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>


<dt>outfile</dt>
<dd>File name of the output file (including extension)
[default 'genalex.csv'].</dd>


<dt>outpath</dt>
<dd>Path where to save the output file [default tempdir()].</dd>


<dt>overwrite</dt>
<dd>If FALSE and filename exists, then the file will not be
overwritten. Set this option to TRUE to overwrite the file [default FALSE].</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: Luis Mijangos, Author: Katrin Hohwieler, wrapper Arthur
Georges (Post to <a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>)

gl2genalex: Converts a genlight object into a format suitable for input to genalex

Description

Usage

Value

Arguments

Author

References

Examples