gl2sa

This function exports a genlight object into a SNPassoc object. See package
SNPassoc for details. This function needs package SNPassoc. At the time of
writing (August 2020) the package was no longer available from CRAN. To
install the package check their github repository.
<a href="https://github.com/isglobal-brge/SNPassoc">https://github.com/isglobal-brge/SNPassoc</a> and/or use
<code>install_github('isglobal-brge/SNPassoc')</code> to install the function and
uncomment the function code.

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

gl2sa function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP data [required].</dd>
<dt>installed</dt>
<dd>Switch to run the function once SNPassoc package i
s installed [default FALSE].#' @param verbose 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>
<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

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

Author

This function exports a genlight object into a SNPassoc object. See package
SNPassoc for details. This function needs package SNPassoc. At the time of
writing (August 2020) the package was no longer available from CRAN. To
install the package check their github repository.
<a href='https://github.com/isglobal-brge/SNPassoc'>https://github.com/isglobal-brge/SNPassoc</a> and/or use
<code>install_github('isglobal-brge/SNPassoc')</code> to install the function and
uncomment the function code.

Converts genlight objects to the format used in the SNPassoc package — gl2sa

<dl>

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


<dt>installed</dt>
<dd>Switch to run the function once SNPassoc package i
s installed [default FALSE].#' @param verbose 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>


<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>

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

gl2sa: Converts genlight objects to the format used in the SNPassoc package

Description

Usage

Value

Arguments

Author

References

See Also