gl.keep.ind

The script, having deleted individuals, optionally identifies resultant
monomorphic loci or loci with all values missing and deletes them
(using gl.filter.monomorphs.r). The script also optionally recalculates
statistics made redundant by the deletion of individuals from the dataset.
The script returns a genlight object with the individuals deleted and,
optionally, the recalculated locus metadata.
See more about data manipulation in the [tutorial](http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial4dartrdatamanipulation22-dec-21-3.pdf).

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

Peter J. Unmack

Oliver Berry

Lindsay V. Clark

Floriaan Devloo-Delva

Eric Archer

gl.keep.ind function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP or presence/absence
(SilicoDArT) data [required].</dd>
<dt>ind.list</dt>
<dd>A list of individuals to be removed [required].</dd>
<dt>recalc</dt>
<dd>Recalculate the locus metadata statistics [default FALSE].</dd>
<dt>mono.rm</dt>
<dd>Remove monomorphic loci [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: Arthur Georges -- Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>

Author

Removes all but the specified individuals from a genlight object — gl.keep.ind

<dl>

<dt>x</dt>
<dd>Name of the genlight object containing the SNP or presence/absence
(SilicoDArT) data [required].</dd>


<dt>ind.list</dt>
<dd>A list of individuals to be removed [required].</dd>


<dt>recalc</dt>
<dd>Recalculate the locus metadata statistics [default FALSE].</dd>


<dt>mono.rm</dt>
<dd>Remove monomorphic loci [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: Arthur Georges -- Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>

gl.keep.ind: Removes all but the specified individuals from a genlight object

Description

Usage

Value

Arguments

Author

See Also

Examples