gl.filter.heterozygosity

Calculates the observed heterozygosity for each individual in a genlight
object and filters individuals based on specified threshold values.
Use gl.report.heterozygosity to determine the appropriate thresholds.

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.filter.heterozygosity function

<dl><dt>x</dt>
<dd>A genlight object containing the SNP genotypes [required].</dd>
<dt>t.upper</dt>
<dd>Filter individuals &gt; the threshold [default 0.7].</dd>
<dt>t.lower</dt>
<dd>Filter individuals &lt; the threshold [default 0].</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, unless specified using gl.set.verbosity].</dd></dl>

Arguments

Custodian: Luis Mijangos -- Post to
<a href="https://groups.google.com/d/forum/dartr">https://groups.google.com/d/forum/dartr</a>

Author

Filters individuals with average heterozygosity greater than a
 specified upper threshold or less than a specified lower threshold
 @family matched filter — gl.filter.heterozygosity

<dl>

<dt>x</dt>
<dd>A genlight object containing the SNP genotypes [required].</dd>


<dt>t.upper</dt>
<dd>Filter individuals &gt; the threshold [default 0.7].</dd>


<dt>t.lower</dt>
<dd>Filter individuals &lt; the threshold [default 0].</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, unless specified using gl.set.verbosity].</dd>

</dl>

Custodian: Luis Mijangos -- Post to
<a href='https://groups.google.com/d/forum/dartr'>https://groups.google.com/d/forum/dartr</a>

Filters individuals with average heterozygosity greater than a
 specified upper threshold or less than a specified lower threshold
 @family matched filter

gl.filter.heterozygosity: Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold @family matched filter

Description

Usage

Value

Arguments

Author

Examples