gl.subsample.loc

A function to subsample loci at random in a genlight object
with and without replacement.

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

gl.subsample.loc function

<dl><dt>x</dt>
<dd>Name of the genlight object containing the SNP or presence/absence
(SilicoDArT) data [required].</dd>
<dt>n</dt>
<dd>Number of loci to include in the subsample [default NULL]</dd>
<dt>replace</dt>
<dd>If TRUE, sampling is with replacement [default TRUE]</dd>
<dt>error.check</dt>
<dd>If TRUE, will undertake error checks on input parameters 
[default TRUE]</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 NULL, unless specified using gl.set.verbosity]</dd></dl>

Arguments

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

Author

Subsample loci from a genlight object — gl.subsample.loc

<dl>

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


<dt>n</dt>
<dd>Number of loci to include in the subsample [default NULL]</dd>


<dt>replace</dt>
<dd>If TRUE, sampling is with replacement [default TRUE]</dd>


<dt>error.check</dt>
<dd>If TRUE, will undertake error checks on input parameters 
[default TRUE]</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 NULL, unless specified using gl.set.verbosity]</dd>

</dl>

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

gl.subsample.loc: Subsample loci from a genlight object

Description

Usage

Value

Arguments

Author

Details

See Also

Examples