gl2snapp

The output nexus file contains the SNP data and relevant PAUP command lines
suitable for BEAUti.

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

gl2snapp 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 "snapp.nex"].</dd>
<dt>outpath</dt>
<dd>Path where to save the output file
[default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.'
when calling this function to direct output files to your working directory.</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

Converts a genlight object to nexus format suitable for phylogenetic analysis
 by SNAPP (via BEAUti) — gl2snapp

<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 "snapp.nex"].</dd>


<dt>outpath</dt>
<dd>Path where to save the output file
[default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.'
when calling this function to direct output files to your working directory.</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>)

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gl2snapp: Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)

Description

Usage

Value

Arguments

Author

References

Examples